May-19 22:29:11.056 [main] DEBUG nextflow.cli.Launcher - $> nextflow run 'https://github.com/nf-core/sarek' -r 2.7.1 -dsl1 -profile test,docker -params-file params.yml -with-tower 'https://tower.sagebionetworks.org/api' -resume May-19 22:29:11.158 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.04.2 May-19 22:29:11.226 [main] DEBUG nextflow.scm.AssetManager - Repository URL: https://github.com/nf-core/sarek; Project: nf-core/sarek; Hub provider: github May-19 22:29:12.735 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/ssm-user/.nextflow/assets/nf-core/sarek/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/sarek.git May-19 22:29:13.423 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ssm-user/.nextflow/assets/nf-core/sarek/nextflow.config May-19 22:29:13.424 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ssm-user/.nextflow/assets/nf-core/sarek/nextflow.config May-19 22:29:13.482 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker` May-19 22:29:14.042 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-19 22:29:14.056 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-19 22:29:14.057 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-19 22:29:14.062 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode May-19 22:29:14.067 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-19 22:29:14.289 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-19 22:29:14.289 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager May-19 22:29:14.514 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, alice, test_annotation, uppmax, abims, test_tool, nihbiowulf, nu_genomics, oist, sahmri, mpcdf, leicester, lugh, cambridge, unibe_ibu, vai, podman, test_umi_qiaseq, czbiohub_aws, jax, cheaha, ccga_med, test, google, computerome, seg_globe, sanger, pasteur, eddie, test_umi_tso, azurebatch, bi, bigpurple, test_trimming, cedars, docker, gis, eva, test_use_gatk_spark, utd_ganymede, charliecloud, fgcz, conda, singularity, icr_davros, munin, rosalind, prince, hasta, hebbe, cfc, utd_sysbio, uzh, debug, genouest, cbe, ebc, ccga_dx, crick, test_split_fastq, marvin, phoenix, biohpc_gen, shifter, awsbatch, uct_hpc, test_targeted, imperial, maestro, aws_tower, binac] May-19 22:29:14.565 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=null from config declaration May-19 22:29:14.566 [main] INFO nextflow.cli.CmdRun - Launching `https://github.com/nf-core/sarek` [hopeful_fermi] DSL1 - revision: 68b9930a74 [2.7.1] May-19 22:29:14.568 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/ssm-user/.nextflow/plugins; core-plugins: nf-amazon@1.7.2,nf-azure@0.13.2,nf-console@1.0.3,nf-ga4gh@1.0.3,nf-google@1.1.4,nf-sqldb@0.4.0,nf-tower@1.4.0 May-19 22:29:14.569 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] May-19 22:29:14.574 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-19 22:29:14.574 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-19 22:29:14.576 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode May-19 22:29:14.588 [main] INFO org.pf4j.AbstractPluginManager - No plugins May-19 22:29:14.589 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-tower version: 1.4.0 May-19 22:29:14.621 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-tower@1.4.0' resolved May-19 22:29:14.622 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-tower@1.4.0' May-19 22:29:14.634 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-tower@1.4.0 May-19 22:29:14.733 [main] DEBUG nextflow.Session - Session uuid: 7cf07177-f89c-4e3a-8c77-c86f353cd0e9 May-19 22:29:14.734 [main] DEBUG nextflow.Session - Run name: hopeful_fermi May-19 22:29:14.735 [main] DEBUG nextflow.Session - Executor pool size: 8 May-19 22:29:14.752 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/ssm-user/.nextflow/assets/nf-core/sarek/nextflow.config May-19 22:29:14.753 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/ssm-user/.nextflow/assets/nf-core/sarek/nextflow.config May-19 22:29:14.754 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,docker` May-19 22:29:15.245 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, genotoul, alice, test_annotation, uppmax, abims, test_tool, nihbiowulf, nu_genomics, oist, sahmri, mpcdf, leicester, lugh, cambridge, unibe_ibu, vai, podman, test_umi_qiaseq, czbiohub_aws, jax, cheaha, ccga_med, test, google, computerome, seg_globe, sanger, pasteur, eddie, test_umi_tso, azurebatch, bi, bigpurple, test_trimming, cedars, docker, gis, eva, test_use_gatk_spark, utd_ganymede, charliecloud, fgcz, conda, singularity, icr_davros, munin, rosalind, prince, hasta, hebbe, cfc, utd_sysbio, uzh, debug, genouest, cbe, ebc, ccga_dx, crick, test_split_fastq, marvin, phoenix, biohpc_gen, shifter, awsbatch, uct_hpc, test_targeted, imperial, maestro, aws_tower, binac] May-19 22:29:15.289 [main] DEBUG nextflow.cli.CmdRun - Version: 22.04.2 build 5701 Created: 16-05-2022 17:52 UTC System: Linux 4.14.232-176.381.amzn2.x86_64 Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.13+8-LTS Encoding: UTF-8 (UTF-8) Process: 6184@ip-10-41-26-113.ec2.internal [10.41.26.113] CPUs: 8 - Mem: 62.3 GB (46.8 GB) - Swap: 0 (0) May-19 22:29:15.311 [main] DEBUG nextflow.Session - Work-dir: /home/ssm-user/reprex/work [xfs] May-19 22:29:15.328 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] May-19 22:29:15.345 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory May-19 22:29:15.370 [main] DEBUG nextflow.Session - Observer factory: TowerFactory May-19 22:29:15.526 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory May-19 22:29:15.540 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 May-19 22:29:15.705 [main] DEBUG nextflow.Session - Session start invoked May-19 22:29:15.711 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/ssm-user/reprex/results/pipeline_info/pipeline_dag_2022-05-19_22-29-14.svg May-19 22:29:15.724 [main] DEBUG io.seqera.tower.plugin.TowerClient - Creating Tower observer -- endpoint=https://tower.sagebionetworks.org/api; requestInterval=1s; aliveInterval=1m; maxRetries=5; backOffBase=3; backOffDelay=250 May-19 22:29:15.895 [main] DEBUG nextflow.Session - Using default localLib path: /home/ssm-user/.nextflow/assets/nf-core/sarek/lib May-19 22:29:15.902 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ssm-user/.nextflow/assets/nf-core/sarek/lib May-19 22:29:15.903 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/ssm-user/.nextflow/assets/nf-core/sarek/lib/nfcore_external_java_deps.jar May-19 22:29:23.982 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution May-19 22:29:24.002 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' ____ .´ _ `. / |\`-_ \  __ __ ___  | | \ `-| |__` /\ |__) |__ |__/ \ | \ / .__| /¯¯\ | \ |___ | \ `|____\´  nf-core/sarek v2.7.1 ------------------------------------------------------ May-19 22:29:24.374 [main] INFO nextflow.Nextflow - Core Nextflow options revision : 2.7.1 runName : hopeful_fermi containerEngine : docker container : nfcore/sarek:2.7.1 launchDir : /home/ssm-user/reprex workDir : /home/ssm-user/reprex/work projectDir : /home/ssm-user/.nextflow/assets/nf-core/sarek userName : ssm-user profile : test,docker configFiles : /home/ssm-user/.nextflow/assets/nf-core/sarek/nextflow.config Input/output options input : https://gist.githubusercontent.com/BrunoGrandePhD/6869bf506e6acf7b920a22b666f4e443/raw/ff7ea0757ebbd324cd125b1d48f54e6ec9f969c9/sarek-test.tsv Main options tools : null no_intervals : true skip_qc : bamqc,baserecalibrator,bcftools,documentation,fastqc,markduplicates,multiqc,samtools,sentieon,vcftools,versions Trim/split FASTQ clip_r1 : 0 clip_r2 : 0 three_prime_clip_r1 : 0 three_prime_clip_r2 : 0 trim_nextseq : 0 Preprocessing markdup_java_options : "-Xms4000m -Xmx7g" skip_markduplicates : true Variant Calling ascat_ploidy : null ascat_purity : null cf_contamination : null cf_ploidy : 2 read_structure1 : null read_structure2 : null Annotation annotate_tools : null cadd_indels : false cadd_indels_tbi : false cadd_wg_snvs : false cadd_wg_snvs_tbi : false snpeff_cache : null vep_cache : null Reference genome options genome : smallGRCh37 dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz fasta : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta intervals : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/small.intervals snpeff_db : WBcel235.86 species : caenorhabditis_elegans vep_cache_version : 99 igenomes_base : s3://ngi-igenomes/igenomes/ genomes_base : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference igenomes_ignore : true Generic options max_multiqc_email_size : 25 MB sequencing_center : null Max job request options single_cpu_mem : 7 GB max_cpus : 2 max_memory : 6 GB max_time : 2d Institutional config options config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function ------------------------------------------------------ Only displaying parameters that differ from defaults. ------------------------------------------------------ May-19 22:29:24.381 [main] INFO nextflow.Nextflow - Pipeline Release : 2.7.1 Run Name : hopeful_fermi Max Resources : 6 GB memory, 2 cpus, 2d time per job Container : docker - nfcore/sarek:2.7.1 Output dir : ./results Launch dir : /home/ssm-user/reprex Working dir : /home/ssm-user/reprex/work Script dir : /home/ssm-user/.nextflow/assets/nf-core/sarek User : ssm-user Input : https://gist.githubusercontent.com/BrunoGrandePhD/6869bf506e6acf7b920a22b666f4e443/raw/ff7ea0757ebbd324cd125b1d48f54e6ec9f969c9/sarek-test.tsv Step : mapping Genome : smallGRCh37 Intervals : Do not use Nucleotides/s : 1000 QC tools skipped : bamqc, baserecalibrator, bcftools, documentation, fastqc, markduplicates, multiqc, samtools, sentieon, vcftools, versions MarkDuplicates : Options Java options : "-Xms4000m -Xmx7g" GATK Spark : No Save BAMs mapped : No Skip MarkDuplicates: Yes AWS iGenomes : Do not use Save Reference : No dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz fasta reference : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta intervals : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/small.intervals snpEff DB : WBcel235.86 species : caenorhabditis_elegans VEP cache version : 99 Publish dir mode : copy Config Profile : test,docker Config Description: Minimal test dataset to check pipeline function Config Files : /home/ssm-user/.nextflow/assets/nf-core/sarek/nextflow.config May-19 22:29:24.382 [main] INFO nextflow.Nextflow - ---------------------------------------------------- May-19 22:29:24.506 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:get_software_versions` matches process get_software_versions May-19 22:29:24.509 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.509 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.518 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local May-19 22:29:24.526 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=62.3 GB; capacity=8; pollInterval=100ms; dumpInterval=5m May-19 22:29:24.640 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.640 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.663 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.663 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.678 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.679 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.697 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.697 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.714 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.714 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.748 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.748 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.773 [main] DEBUG nextflow.processor.TaskProcessor - Creating *combiner* operator for each param(s) at index(es): [0] May-19 22:29:24.787 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.788 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.808 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.809 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.836 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.836 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.849 [Actor Thread 10] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=4; maxSize=4; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-19 22:29:24.890 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:24.913 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:24.927 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_2` matches labels `FastQC,cpus_2` for process with name FastQCFQ May-19 22:29:24.927 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:FastQC` matches labels `FastQC,cpus_2` for process with name FastQCFQ May-19 22:29:24.928 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.928 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.947 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_2` matches labels `FastQC,cpus_2` for process with name FastQCBAM May-19 22:29:24.948 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:FastQC` matches labels `FastQC,cpus_2` for process with name FastQCBAM May-19 22:29:24.948 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:24.948 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:24.949 [Actor Thread 3] DEBUG nextflow.util.CacheHelper - [WARN] Unknown hashing type: class nextflow.util.MemoryUnit May-19 22:29:25.048 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.048 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.089 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.090 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.128 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.141 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.141 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.162 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.162 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.180 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.180 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.213 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max` for process with name MapReads May-19 22:29:25.213 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MapReads` matches process MapReads May-19 22:29:25.214 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.214 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.256 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_MapReads May-19 22:29:25.256 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_MapReads May-19 22:29:25.257 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.257 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.261 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.277 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.289 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_8` matches labels `cpus_8` for process with name MergeBamMapped May-19 22:29:25.290 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.290 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.307 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_8` matches labels `cpus_8` for process with name IndexBamMergedForSentieon May-19 22:29:25.308 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.308 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.326 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.328 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_8` matches labels `cpus_8` for process with name IndexBamFile May-19 22:29:25.329 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.329 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.332 [Actor Thread 3] INFO nextflow.processor.TaskProcessor - [d8/24da05] Cached process > BuildDict (human_g1k_v37_decoy.small.fasta) May-19 22:29:25.339 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [ba/f220ab] Cached process > BuildFastaFai (human_g1k_v37_decoy.small.fasta) May-19 22:29:25.340 [Actor Thread 12] INFO nextflow.processor.TaskProcessor - [24/63640b] Cached process > BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz) May-19 22:29:25.370 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [24/c12438] Cached process > BuildBWAindexes (human_g1k_v37_decoy.small.fasta) May-19 22:29:25.390 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.453 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.459 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_16` matches labels `cpus_16` for process with name MarkDuplicates May-19 22:29:25.460 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.460 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.552 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.581 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_Dedup May-19 22:29:25.582 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_Dedup May-19 22:29:25.583 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.583 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.589 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.597 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name BaseRecalibrator May-19 22:29:25.598 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.598 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.599 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.645 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.678 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_2` matches labels `memory_singleCPU_2_task,cpus_2` for process with name GatherBQSRReports May-19 22:29:25.678 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_singleCPU_2_task` matches labels `memory_singleCPU_2_task,cpus_2` for process with name GatherBQSRReports May-19 22:29:25.679 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.679 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.718 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.738 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_2` matches labels `memory_singleCPU_2_task,cpus_2` for process with name ApplyBQSR May-19 22:29:25.739 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_singleCPU_2_task` matches labels `memory_singleCPU_2_task,cpus_2` for process with name ApplyBQSR May-19 22:29:25.739 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.739 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.747 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.747 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.764 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.779 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:25.780 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_BQSR May-19 22:29:25.781 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_BQSR May-19 22:29:25.781 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.782 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.806 [Actor Thread 4] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:25.806 [Actor Thread 10] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:25.808 [Actor Thread 10] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:25.817 [Actor Thread 10] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:25.825 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_8` matches labels `cpus_8` for process with name MergeBamRecal May-19 22:29:25.828 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.829 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.841 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:25.844 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_8` matches labels `cpus_8` for process with name IndexBamRecal May-19 22:29:25.845 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.845 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.855 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.863 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.888 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:25.901 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_2` matches labels `cpus_2` for process with name SamtoolsStats May-19 22:29:25.901 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.901 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.920 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.921 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_16` matches labels `memory_max,cpus_16` for process with name BamQC May-19 22:29:25.923 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.922 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `memory_max,cpus_16` for process with name BamQC May-19 22:29:25.928 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.928 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.943 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_2` matches labels `memory_singleCPU_task_sq,cpus_2` for process with name HaplotypeCaller May-19 22:29:25.943 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_singleCPU_task_sq` matches labels `memory_singleCPU_task_sq,cpus_2` for process with name HaplotypeCaller May-19 22:29:25.943 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.943 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.954 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:25.958 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:25.963 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:25.964 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.964 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.979 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_DNAseq May-19 22:29:25.979 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_DNAseq May-19 22:29:25.980 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.980 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:25.996 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:25.997 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_DNAscope May-19 22:29:25.998 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_DNAscope May-19 22:29:25.998 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:25.998 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.007 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max` for process with name StrelkaSingle May-19 22:29:26.007 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max` for process with name StrelkaSingle May-19 22:29:26.008 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.008 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.016 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max` for process with name MantaSingle May-19 22:29:26.016 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max` for process with name MantaSingle May-19 22:29:26.017 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:26.017 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.017 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.021 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:26.037 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.037 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.043 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:26.046 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name FreebayesSingle May-19 22:29:26.046 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.046 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.069 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:26.093 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:26.099 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name FreeBayes May-19 22:29:26.099 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.099 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.104 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:26.112 [Task submitter] INFO nextflow.Session - [de/5a419f] Submitted process > MapReads (S001-S001-1234N_M2) May-19 22:29:26.118 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name Mutect2 May-19 22:29:26.119 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.119 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.140 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name Mutect2Single May-19 22:29:26.140 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.140 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.150 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:26.155 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:26.159 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:26.159 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.159 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.164 [Task submitter] INFO nextflow.Session - [d6/6895a7] Submitted process > MapReads (S007-S007-9876T_M2) May-19 22:29:26.178 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:26.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_8` matches labels `concat_vcf,cpus_8` for process with name ConcatVCF May-19 22:29:26.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:concat_vcf` matches labels `concat_vcf,cpus_8` for process with name ConcatVCF May-19 22:29:26.185 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.186 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.195 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:26.195 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:26.196 [Task submitter] INFO nextflow.Session - [d4/d52e94] Submitted process > MapReads (S002-S002-1234N_M4) May-19 22:29:26.199 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_8` matches labels `concat_vcf,cpus_8` for process with name ConcatVCF_Mutect2 May-19 22:29:26.199 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:concat_vcf` matches labels `concat_vcf,cpus_8` for process with name ConcatVCF_Mutect2 May-19 22:29:26.199 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.200 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.212 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:26.217 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name PileupSummariesForMutect2 May-19 22:29:26.218 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.218 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.232 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name MergePileupSummaries May-19 22:29:26.232 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.232 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.244 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name CalculateContamination May-19 22:29:26.245 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.245 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.249 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:26.252 [Task submitter] INFO nextflow.Session - [f0/bfdb47] Submitted process > MapReads (S004-S004-1234N_M6) May-19 22:29:26.267 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:26.293 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name FilterMutect2Calls May-19 22:29:26.293 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.293 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.300 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:26.302 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:26.305 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_TNscope May-19 22:29:26.305 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max,sentieon` for process with name Sentieon_TNscope May-19 22:29:26.306 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.306 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.320 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.320 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.334 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max` for process with name Strelka May-19 22:29:26.335 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max` for process with name Strelka May-19 22:29:26.335 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.335 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.344 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:26.348 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max` for process with name Manta May-19 22:29:26.348 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max` for process with name Manta May-19 22:29:26.349 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.349 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.364 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:26.369 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_max` matches labels `cpus_max,memory_max` for process with name StrelkaBP May-19 22:29:26.369 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_max,memory_max` for process with name StrelkaBP May-19 22:29:26.370 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.370 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.386 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:26.386 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.386 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.393 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1,memory_max,msisensor` for process with name MSIsensor_scan May-19 22:29:26.394 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_1,memory_max,msisensor` for process with name MSIsensor_scan May-19 22:29:26.394 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:msisensor` matches labels `cpus_1,memory_max,msisensor` for process with name MSIsensor_scan May-19 22:29:26.394 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.394 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.407 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_4` matches labels `cpus_4,memory_max,msisensor` for process with name MSIsensor_msi May-19 22:29:26.408 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_4,memory_max,msisensor` for process with name MSIsensor_msi May-19 22:29:26.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:msisensor` matches labels `cpus_4,memory_max,msisensor` for process with name MSIsensor_msi May-19 22:29:26.409 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.409 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.411 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:26.420 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_4` matches labels `cpus_4,memory_max,msisensor` for process with name MSIsensor_msiSingle May-19 22:29:26.420 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_max` matches labels `cpus_4,memory_max,msisensor` for process with name MSIsensor_msiSingle May-19 22:29:26.420 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:msisensor` matches labels `cpus_4,memory_max,msisensor` for process with name MSIsensor_msiSingle May-19 22:29:26.421 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.421 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.451 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:26.455 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_singleCPU_2_task` matches labels `memory_singleCPU_2_task` for process with name AlleleCounter May-19 22:29:26.466 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.466 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.480 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:26.488 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_singleCPU_2_task` matches labels `memory_singleCPU_2_task` for process with name ConvertAlleleCounts May-19 22:29:26.489 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.489 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.498 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_singleCPU_2_task` matches labels `memory_singleCPU_2_task` for process with name Ascat May-19 22:29:26.499 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.499 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.513 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1,memory_singleCPU_2_task` for process with name Mpileup May-19 22:29:26.513 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_singleCPU_2_task` matches labels `cpus_1,memory_singleCPU_2_task` for process with name Mpileup May-19 22:29:26.513 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.513 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.533 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name MergeMpileup May-19 22:29:26.534 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.534 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.544 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:26.558 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_8` matches labels `cpus_8` for process with name ControlFREEC May-19 22:29:26.559 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.559 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.573 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_8` matches labels `cpus_8` for process with name ControlFREECSingle May-19 22:29:26.574 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.574 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.586 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_singleCPU_2_task` matches labels `memory_singleCPU_2_task` for process with name ControlFreecViz May-19 22:29:26.586 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.586 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.595 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:memory_singleCPU_2_task` matches labels `memory_singleCPU_2_task` for process with name ControlFreecVizSingle May-19 22:29:26.596 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.596 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.604 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:26.639 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name BcftoolsStats May-19 22:29:26.639 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.640 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.646 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_1` matches labels `cpus_1` for process with name Vcftools May-19 22:29:26.647 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.647 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.653 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:26.661 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:Snpeff` matches process Snpeff May-19 22:29:26.662 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.662 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.665 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:26.675 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.675 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.685 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_4` matches labels `VEP,cpus_4` for process with name VEP May-19 22:29:26.685 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:VEP` matches labels `VEP,cpus_4` for process with name VEP May-19 22:29:26.686 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.686 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.696 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:26.716 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:cpus_4` matches labels `VEP,cpus_4` for process with name VEPmerge May-19 22:29:26.717 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:VEP` matches labels `VEP,cpus_4` for process with name VEPmerge May-19 22:29:26.717 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.717 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.736 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.736 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.738 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:26.764 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:26.814 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:26.840 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MultiQC` matches process MultiQC May-19 22:29:26.840 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.840 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.840 [Actor Thread 57] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.002 s; external sort time: 0.003 s; total time: 0.005 s May-19 22:29:26.841 [Actor Thread 57] DEBUG nextflow.file.FileCollector - >> temp file exists? false May-19 22:29:26.841 [Actor Thread 57] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /tmp/89f875e65fe8e9195ecd1c63266f4891.collect-file May-19 22:29:26.845 [Actor Thread 57] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/89f875e65fe8e9195ecd1c63266f4891.collect-file May-19 22:29:26.854 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-19 22:29:26.854 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-19 22:29:26.857 [Actor Thread 57] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-6451948052833317463 May-19 22:29:26.865 [main] DEBUG nextflow.Session - Workflow process names [dsl1]: FreebayesSingle, VEP, Mpileup, MapReads, MergeMutect2Stats, UMIMapBamFile, ApplyBQSR, IndexBamRecal, Ascat, AlleleCounter, Vcftools, Sentieon_BQSR, BuildGermlineResourceIndex, TrimGalore, Snpeff, BuildKnownIndelsIndex, GroupReadsByUmi, StrelkaSingle, Sentieon_TNscope, HaplotypeCaller, Sentieon_DNAseq, StrelkaBP, Output_documentation, ControlFREEC, BuildIntervals, PileupSummariesForMutect2, ControlFREECSingle, MantaSingle, BuildPonIndex, ControlFreecViz, CompressVCFvep, BuildFastaFai, CalculateContamination, VEPmerge, IndexBamFile, Mutect2Single, BcftoolsStats, Strelka, MergePileupSummaries, UMIFastqToBAM, IndexBamMergedForSentieon, MergeBamMapped, BuildDict, FastQCFQ, Manta, BamQC, GenotypeGVCFs, CompressVCFsnpEff, CreateIntervalBeds, MergeMpileup, GatherBQSRReports, BuildDbsnpIndex, get_software_versions, TIDDIT, FastQCBAM, MarkDuplicates, MSIsensor_msi, BaseRecalibrator, CNVkit, MultiQC, MergeBamRecal, SamtoolsStats, BuildBWAindexes, FreeBayes, CompressSentieonVCF, ConvertAlleleCounts, ControlFreecVizSingle, CallMolecularConsensusReads, Sentieon_MapReads, Mutect2, ConcatVCF, Sentieon_DNAscope, FilterMutect2Calls, MSIsensor_scan, MSIsensor_msiSingle, Sentieon_Dedup, ConcatVCF_Mutect2 May-19 22:29:26.866 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:26.921 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:26.928 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:26.962 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:26.992 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:27.025 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:27.038 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:27.093 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:27.114 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.150 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.151 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.185 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.203 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.223 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.241 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:27.254 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.274 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.315 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.344 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.375 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.399 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:27.446 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.458 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:27.485 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:27.501 [main] INFO io.seqera.tower.plugin.TowerClient - Monitor the execution with Nextflow Tower using this url https://tower.sagebionetworks.org/orgs/Sage-Bionetworks/workspaces/example-project/watch/1GsSi5Qpe0SsW5 May-19 22:29:27.504 [main] DEBUG nextflow.script.ScriptRunner - > Await termination May-19 22:29:27.504 [main] DEBUG nextflow.Session - Session await May-19 22:29:27.533 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:27.553 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:27.589 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.612 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.638 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.686 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.704 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.718 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:27.738 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.773 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:27.798 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:27.826 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:27.851 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:27.889 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:27.911 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:27.947 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:27.964 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:27.988 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:28.009 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:28.057 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.069 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:28.085 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:28.105 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:28.112 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:28.124 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:28.136 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:28.185 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:28.283 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.295 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:28.329 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.372 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.389 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:28.415 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.424 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:28.451 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:28.478 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:28.513 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:28.522 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: MapReads (S001-S001-1234N_M2); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/de/5a419f97d66f5b80b7ff5633f644e1] May-19 22:29:28.523 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.543 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:28.551 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:28.554 [Task submitter] INFO nextflow.Session - [f3/980158] Submitted process > MapReads (S003-S003-1234N_M5) May-19 22:29:28.588 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:28.594 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: MapReads (S002-S002-1234N_M4); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/d4/d52e948a07fd6896a489ebd81a5d70] May-19 22:29:28.602 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:28.615 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:28.622 [Task submitter] INFO nextflow.Session - [80/7c470a] Submitted process > MapReads (S005-S005-1234N_M7) May-19 22:29:28.681 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:28.696 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:28.734 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.745 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.765 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 56; name: MapReads (S007-S007-9876T_M2); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/d6/6895a7344e597ad38df2ec9b881705] May-19 22:29:28.768 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:28.772 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:28.791 [Actor Thread 41] INFO nextflow.processor.TaskProcessor - [04/a9f36d] Cached process > MapReads (S013-S013-1234N_M5) May-19 22:29:28.797 [Task submitter] INFO nextflow.Session - [39/05a47b] Submitted process > MapReads (S000-S000-1234N_M1) May-19 22:29:28.805 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:28.820 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.847 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:28.866 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: MapReads (S004-S004-1234N_M6); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/f0/bfdb472dcc1c24232deab8426a2e1e] May-19 22:29:28.874 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:28.874 [Task submitter] INFO nextflow.Session - [25/30f888] Submitted process > MapReads (S006-S006-9876T_M1) May-19 22:29:28.890 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:28.902 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:28.932 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.937 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:28.947 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:28.992 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:28.999 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.029 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:29.050 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:29.085 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:29.100 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:29.113 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:29.136 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.186 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.209 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:29.224 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:29.230 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:29.273 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.296 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:29.349 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.360 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:29.388 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:29.399 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.418 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:29.456 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:29.471 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:29.484 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:29.504 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:29.524 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:29.535 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:29.544 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:29.557 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:29.566 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:29.592 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.604 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:29.618 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:29.635 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.662 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:29.706 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.756 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:29.780 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:29.830 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.865 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:29.904 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:29.916 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:29.992 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.063 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.086 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.111 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.154 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:30.185 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:30.240 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.253 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.274 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.307 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.342 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.360 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.368 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:30.378 [Actor Thread 41] INFO nextflow.processor.TaskProcessor - [ef/7309f0] Cached process > MapReads (S024-S024-1234N_M6) May-19 22:29:30.387 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.417 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.429 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.439 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.471 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.494 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.535 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:30.571 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:30.593 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:30.602 [Actor Thread 55] INFO nextflow.processor.TaskProcessor - [52/e5810f] Cached process > MapReads (S038-S038-9876T_M3) May-19 22:29:30.606 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:30.622 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:30.644 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:30.656 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:30.671 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:30.680 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:30.690 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [75/741061] Cached process > MapReads (S037-S037-9876T_M2) May-19 22:29:30.704 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.738 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:30.746 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.755 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [b6/a6d1d1] Cached process > MapReads (S035-S035-1234N_M7) May-19 22:29:30.769 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.770 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.777 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:30.787 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [fa/47a2bf] Cached process > MapReads (S034-S034-1234N_M6) May-19 22:29:30.802 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.822 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:30.835 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.838 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.842 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [a8/61c8e4] Cached process > MapReads (S032-S032-1234N_M4) May-19 22:29:30.859 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:30.875 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:30.884 [Actor Thread 40] INFO nextflow.processor.TaskProcessor - [8d/53f8a9] Cached process > MapReads (S033-S033-1234N_M5) May-19 22:29:30.887 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:30.909 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:30.922 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:30.951 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:30.962 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:30.981 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:30.990 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: MapReads (S005-S005-1234N_M7); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/80/7c470a61c5b5ca8436ac539ce9c57f] May-19 22:29:31.008 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:31.009 [Task submitter] INFO nextflow.Session - [c3/5f34d0] Submitted process > MapReads (S012-S012-1234N_M4) May-19 22:29:31.019 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.039 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:31.061 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:31.068 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.078 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: MapReads (S003-S003-1234N_M5); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/f3/980158b92d938f4642ae9abdd97085] May-19 22:29:31.085 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:31.086 [Task submitter] INFO nextflow.Session - [d2/c449e0] Submitted process > MapReads (S010-S010-1234N_M1) May-19 22:29:31.113 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: MapReads (S000-S000-1234N_M1); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/39/05a47b4757f74fd9beac7bf9629147] May-19 22:29:31.115 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.119 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:31.119 [Task submitter] INFO nextflow.Session - [0e/d0a962] Submitted process > MapReads (S008-S008-9876T_M3) May-19 22:29:31.133 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:31.134 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.140 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [57/b70157] Cached process > MapReads (S045-S045-1234N_M7) May-19 22:29:31.155 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.166 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.173 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: MapReads (S006-S006-9876T_M1); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/25/30f8882f123cc13d7da5b69f26be4a] May-19 22:29:31.184 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:31.185 [Task submitter] INFO nextflow.Session - [f4/f0632b] Submitted process > MapReads (S018-S018-9876T_M3) May-19 22:29:31.202 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.301 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:31.316 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.321 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [c7/12e851] Cached process > MapReads (S043-S043-1234N_M5) May-19 22:29:31.370 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.392 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:31.403 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [99/deb820] Cached process > MapReads (S042-S042-1234N_M4) May-19 22:29:31.450 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.481 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.483 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.501 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:31.512 [Actor Thread 58] INFO nextflow.processor.TaskProcessor - [e9/3dff01] Cached process > MapReads (S040-S040-1234N_M1) May-19 22:29:31.514 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:31.525 [Actor Thread 48] INFO nextflow.processor.TaskProcessor - [cb/cd4cfd] Cached process > MapReads (S036-S036-9876T_M1) May-19 22:29:31.559 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.595 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.611 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.644 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.694 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:31.702 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:31.704 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:31.714 [Actor Thread 24] INFO nextflow.processor.TaskProcessor - [8f/edc702] Cached process > MapReads (S039-S039-9876T_M4) May-19 22:29:31.737 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.756 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.761 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:31.780 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:31.798 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:31.804 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [ef/8f9e4f] Cached process > MapReads (S049-S049-9876T_M4) May-19 22:29:31.814 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:31.831 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:31.849 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:31.871 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:31.881 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [e6/18078f] Cached process > MapReads (S048-S048-9876T_M3) May-19 22:29:31.912 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:31.939 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:31.945 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [39/a6229b] Cached process > MapReads (S041-S041-1234N_M2) May-19 22:29:31.961 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:31.983 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:31.987 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.006 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:32.012 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [f6/755367] Cached process > MapReads (S044-S044-1234N_M6) May-19 22:29:32.020 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.034 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.054 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.073 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.108 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:32.112 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.150 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:32.182 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.206 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.233 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.249 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.282 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:32.288 [Actor Thread 46] INFO nextflow.processor.TaskProcessor - [00/a203ef] Cached process > MapReads (S055-S055-1234N_M7) May-19 22:29:32.305 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.307 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.365 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.382 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:32.388 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [d6/78b04a] Cached process > MapReads (S046-S046-9876T_M1) May-19 22:29:32.402 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.409 [Actor Thread 43] INFO nextflow.processor.TaskProcessor - [5d/e73dc0] Cached process > MapReads (S047-S047-9876T_M2) May-19 22:29:32.426 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.469 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:32.483 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:32.492 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.498 [Actor Thread 24] INFO nextflow.processor.TaskProcessor - [3f/d6d77b] Cached process > MapReads (S051-S051-1234N_M2) May-19 22:29:32.522 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.531 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.538 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.553 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.578 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.608 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.618 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:32.626 [Actor Thread 44] INFO nextflow.processor.TaskProcessor - [19/d5fd5a] Cached process > MapReads (S050-S050-1234N_M1) May-19 22:29:32.646 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:32.714 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.717 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:32.723 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [ac/6308d8] Cached process > MapReads (S058-S058-9876T_M3) May-19 22:29:32.741 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:32.762 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:32.762 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.769 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [29/fc0bba] Cached process > MapReads (S057-S057-9876T_M2) May-19 22:29:32.780 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:32.794 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.816 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:32.822 [Actor Thread 58] INFO nextflow.processor.TaskProcessor - [46/6b9b79] Cached process > MapReads (S054-S054-1234N_M6) May-19 22:29:32.829 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [e0/ebb92a] Cached process > MapReads (S052-S052-1234N_M4) May-19 22:29:32.844 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.845 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.858 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.874 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.897 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.907 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:32.924 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:32.935 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:32.954 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.963 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:32.986 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:32.994 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.012 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.015 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.020 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [3f/d5836f] Cached process > MapReads (S064-S064-1234N_M6) May-19 22:29:33.038 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.043 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.047 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 68; name: MapReads (S012-S012-1234N_M4); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/c3/5f34d03d84acbfd14bb1bf4bfa613c] May-19 22:29:33.054 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.058 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:33.058 [Task submitter] INFO nextflow.Session - [6a/b4d22e] Submitted process > MapReads (S009-S009-9876T_M4) May-19 22:29:33.061 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [f3/b98b76] Cached process > MapReads (S053-S053-1234N_M5) May-19 22:29:33.061 [Actor Thread 41] INFO nextflow.processor.TaskProcessor - [63/ddd1bf] Cached process > MapReads (S062-S062-1234N_M4) May-19 22:29:33.080 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.093 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.097 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.103 [Actor Thread 45] INFO nextflow.processor.TaskProcessor - [71/634d10] Cached process > MapReads (S061-S061-1234N_M2) May-19 22:29:33.114 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:33.128 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.132 [Actor Thread 46] INFO nextflow.processor.TaskProcessor - [25/867709] Cached process > MapReads (S056-S056-9876T_M1) May-19 22:29:33.150 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.172 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.181 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.186 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [bd/0a407e] Cached process > MapReads (S060-S060-1234N_M1) May-19 22:29:33.204 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:33.221 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:33.233 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.237 [Actor Thread 55] INFO nextflow.processor.TaskProcessor - [47/2d6ad7] Cached process > MapReads (S059-S059-9876T_M4) May-19 22:29:33.238 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.253 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.285 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:33.306 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:33.328 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.340 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.352 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.379 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.385 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.389 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 57; name: MapReads (S008-S008-9876T_M3); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/0e/d0a9620a152b14366fbba58af2fa37] May-19 22:29:33.396 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:33.396 [Task submitter] INFO nextflow.Session - [10/8066bf] Submitted process > MapReads (S017-S017-9876T_M2) May-19 22:29:33.403 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.421 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:33.436 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: MapReads (S010-S010-1234N_M1); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/d2/c449e048452b8c4ff33c7fc314ee41] May-19 22:29:33.440 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:33.442 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:33.443 [Task submitter] INFO nextflow.Session - [f9/13e62d] Submitted process > MapReads (S016-S016-9876T_M1) May-19 22:29:33.453 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.458 [Actor Thread 44] INFO nextflow.processor.TaskProcessor - [59/422808] Cached process > MapReads (S069-S069-9876T_M4) May-19 22:29:33.467 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:33.482 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:33.488 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.493 [Actor Thread 45] INFO nextflow.processor.TaskProcessor - [b1/42b1e9] Cached process > MapReads (S068-S068-9876T_M3) May-19 22:29:33.504 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:33.518 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:33.527 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.532 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [24/f67b85] Cached process > MapReads (S066-S066-9876T_M1) May-19 22:29:33.533 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: MapReads (S018-S018-9876T_M3); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/f4/f0632b74f7d736240f198c00e11325] May-19 22:29:33.549 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:33.550 [Task submitter] INFO nextflow.Session - [d0/2b76da] Submitted process > MapReads (S014-S014-1234N_M6) May-19 22:29:33.562 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:33.575 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:33.587 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.592 [Actor Thread 48] INFO nextflow.processor.TaskProcessor - [59/ccd17d] Cached process > MapReads (S067-S067-9876T_M2) May-19 22:29:33.610 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.629 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.635 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.648 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.653 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [d3/2044a3] Cached process > MapReads (S063-S063-1234N_M5) May-19 22:29:33.679 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:33.687 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:33.724 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:33.765 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.766 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.771 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [05/e8087c] Cached process > MapReads (S065-S065-1234N_M7) May-19 22:29:33.779 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.783 [Actor Thread 48] INFO nextflow.processor.TaskProcessor - [92/04de61] Cached process > MapReads (S075-S075-1234N_M7) May-19 22:29:33.799 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.838 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.841 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.843 [Actor Thread 41] INFO nextflow.processor.TaskProcessor - [65/e35925] Cached process > MapReads (S074-S074-1234N_M6) May-19 22:29:33.853 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.857 [Actor Thread 45] INFO nextflow.processor.TaskProcessor - [aa/69e3c0] Cached process > MapReads (S073-S073-1234N_M5) May-19 22:29:33.880 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.893 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:33.913 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:33.927 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:33.970 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:33.977 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [b9/dbf385] Cached process > MapReads (S070-S070-1234N_M1) May-19 22:29:33.981 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:33.999 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.039 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.092 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.101 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.104 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.114 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.126 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:34.132 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [ad/fd17e6] Cached process > MapReads (S071-S071-1234N_M2) May-19 22:29:34.144 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.171 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.172 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.186 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:34.194 [Actor Thread 45] INFO nextflow.processor.TaskProcessor - [2f/f3c27d] Cached process > MapReads (S080-S080-1234N_M1) May-19 22:29:34.231 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:34.242 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:34.262 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:34.267 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:34.272 [Actor Thread 58] INFO nextflow.processor.TaskProcessor - [c2/9547a5] Cached process > MapReads (S072-S072-1234N_M4) May-19 22:29:34.306 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:34.309 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:34.330 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:34.342 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:34.346 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:34.351 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [59/5e5d06] Cached process > MapReads (S076-S076-9876T_M1) May-19 22:29:34.393 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.412 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.425 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.438 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.453 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:34.457 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [39/d381a2] Cached process > MapReads (S077-S077-9876T_M2) May-19 22:29:34.457 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [c1/0e88ae] Cached process > MapReads (S084-S084-1234N_M6) May-19 22:29:34.468 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.511 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.515 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:34.524 [Actor Thread 48] INFO nextflow.processor.TaskProcessor - [b5/3edf20] Cached process > MapReads (S078-S078-9876T_M3) May-19 22:29:34.524 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [ec/ae8078] Cached process > MapReads (S083-S083-1234N_M5) May-19 22:29:34.552 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.568 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.590 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:34.595 [Actor Thread 41] INFO nextflow.processor.TaskProcessor - [48/175566] Cached process > MapReads (S079-S079-9876T_M4) May-19 22:29:34.611 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [ff/6e0c44] Cached process > MapReads (S082-S082-1234N_M4) May-19 22:29:34.630 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.636 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.662 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.721 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.738 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b6/8eb24b60a3aa6154124e77caf3e733/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.749 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/53/b9f58fd51bcb7c62cc8a7ae3569a82/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.800 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:34.806 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [d3/9d710b] Cached process > MapReads (S081-S081-1234N_M2) May-19 22:29:34.816 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [f7/0e9e66] Cached process > MapReads (S091-S091-1234N_M2) May-19 22:29:34.824 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.958 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:34.970 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.985 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/c2/696fd4cb5d77789798126869bb7006/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:34.993 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/a6/11b897ce8feb6c04df60bd186b240d/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.001 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.006 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [13/f169bc] Cached process > MapReads (S090-S090-1234N_M1) May-19 22:29:35.013 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.029 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.042 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.042 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.053 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.059 [Actor Thread 16] INFO nextflow.processor.TaskProcessor - [1d/3a12c2] Cached process > MapReads (S088-S088-9876T_M3) May-19 22:29:35.067 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.087 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.098 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.106 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [4d/b6e12a] Cached process > MapReads (S087-S087-9876T_M2) May-19 22:29:35.120 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.130 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.161 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.166 [Actor Thread 58] INFO nextflow.processor.TaskProcessor - [67/e89f37] Cached process > MapReads (S086-S086-9876T_M1) May-19 22:29:35.175 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.178 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 65; name: MapReads (S009-S009-9876T_M4); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/6a/b4d22e83c213e11ed6d6115c9918fe] May-19 22:29:35.182 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:35.183 [Task submitter] INFO nextflow.Session - [09/484d99] Submitted process > MapReads (S023-S023-1234N_M5) May-19 22:29:35.193 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.211 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:35.216 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.233 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.237 [Actor Thread 40] INFO nextflow.processor.TaskProcessor - [ed/f41709] Cached process > MapReads (S085-S085-1234N_M7) May-19 22:29:35.243 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.271 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.288 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.289 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.317 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:35.326 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.341 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.366 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.367 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.372 [Actor Thread 58] INFO nextflow.processor.TaskProcessor - [85/8dbc4b] Cached process > MapReads (S097-S097-9876T_M2) May-19 22:29:35.377 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/7d/be3566d6d05024d3a7f13f88f2d382/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.384 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fc/c16a2ffcdb4eeec155b59b507783e4/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.395 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.400 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [5f/40ab0e] Cached process > MapReads (S096-S096-9876T_M1) May-19 22:29:35.408 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/3d/62d9c60febd43e9641491ea1b5c04e/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:35.419 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/5e/bd9ce897c07e6e246142f24397ed27/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.426 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.430 [Actor Thread 46] INFO nextflow.processor.TaskProcessor - [73/20da25] Cached process > MapReads (S095-S095-1234N_M7) May-19 22:29:35.436 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:35.450 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.461 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.466 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/48/e850c457fd448df16bb5d992ac501d/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:35.467 [Actor Thread 48] INFO nextflow.processor.TaskProcessor - [53/e30cff] Cached process > MapReads (S089-S089-9876T_M4) May-19 22:29:35.469 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [6f/844185] Cached process > MapReads (S094-S094-1234N_M6) May-19 22:29:35.487 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.509 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:35.512 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.516 [Actor Thread 41] INFO nextflow.processor.TaskProcessor - [70/e8008f] Cached process > MapReads (S093-S093-1234N_M5) May-19 22:29:35.521 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.542 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.547 [Actor Thread 45] INFO nextflow.processor.TaskProcessor - [e9/8bb3f5] Cached process > MapReads (S092-S092-1234N_M4) May-19 22:29:35.556 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/50/8931c1a832570d34c3fd22f111fda4/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:35.575 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/66/6ad1e964ee18014198f655679d1093/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.583 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/b3/8dd3e71970cc3b35a90795c716f0e1/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz May-19 22:29:35.597 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/fa/ab43564e443e906c74c5a76ae56afb/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.606 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/60/443994121ddf2245d96aea40eb2ba9/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz May-19 22:29:35.614 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/80/bc3237f45f64849d77b655368696f4/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.629 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: MapReads (S016-S016-9876T_M1); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/f9/13e62d9f5c1cebcbb7d3151653da95] May-19 22:29:35.638 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:35.638 [Task submitter] INFO nextflow.Session - [9d/19a8d3] Submitted process > MapReads (S022-S022-1234N_M4) May-19 22:29:35.650 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/20/1752bd0aa761ac4d22665c02fedff5/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.664 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.669 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [db/9d5526] Cached process > MapReads (S099-S099-9876T_M4) May-19 22:29:35.685 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/4c/a94310c04dc71f283e69bba2987279/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.691 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/8f/c59f866c89d9de94fb52bbbb1d0946/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.700 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: MapReads (S017-S017-9876T_M2); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/10/8066bf03a3d29d80e75b3d8ab80f3e] May-19 22:29:35.705 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:35.706 [Task submitter] INFO nextflow.Session - [60/60db34] Submitted process > MapReads (S021-S021-1234N_M2) May-19 22:29:35.706 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:35.710 [Actor Thread 40] INFO nextflow.processor.TaskProcessor - [db/afefe2] Cached process > MapReads (S098-S098-9876T_M3) May-19 22:29:35.725 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/2f/bd553fc25c651ddf2f1ea027a2350d/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz May-19 22:29:35.732 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz at /home/ssm-user/reprex/work/stage/25/cb41227695d57b069b79b8c50e35bc/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz May-19 22:29:35.779 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 72; name: MapReads (S014-S014-1234N_M6); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/d0/2b76da40c3d0ba53bc427bb6456159] May-19 22:29:35.792 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:35.792 [Task submitter] INFO nextflow.Session - [7e/f4bdee] Submitted process > MapReads (S015-S015-1234N_M7) May-19 22:29:37.407 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 97; name: MapReads (S023-S023-1234N_M5); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/09/484d9939bbe0c895aafd0f05d7293a] May-19 22:29:37.412 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:37.412 [Task submitter] INFO nextflow.Session - [88/0763d1] Submitted process > MapReads (S019-S019-9876T_M4) May-19 22:29:37.570 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: MapReads (S022-S022-1234N_M4); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/9d/19a8d3aace6771ebf19974b237e504] May-19 22:29:37.575 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: MapReads (S021-S021-1234N_M2); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/60/60db34a23f484dd2ed0025e8070bda] May-19 22:29:37.580 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:37.581 [Task submitter] INFO nextflow.Session - [cf/c36bb9] Submitted process > MapReads (S027-S027-9876T_M2) May-19 22:29:37.596 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:37.597 [Task submitter] INFO nextflow.Session - [6d/0c5960] Submitted process > MapReads (S011-S011-1234N_M2) May-19 22:29:37.635 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 76; name: MapReads (S015-S015-1234N_M7); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/7e/f4bdee6501997d5c368f57e330d309] May-19 22:29:37.640 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:37.640 [Task submitter] INFO nextflow.Session - [e2/e1d97d] Submitted process > MapReads (S031-S031-1234N_M2) May-19 22:29:38.894 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 86; name: MapReads (S019-S019-9876T_M4); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/88/0763d11ac058b309153d452411ad5c] May-19 22:29:38.898 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:38.898 [Task submitter] INFO nextflow.Session - [b0/e5256f] Submitted process > MapReads (S030-S030-1234N_M1) May-19 22:29:38.986 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 110; name: MapReads (S027-S027-9876T_M2); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/cf/c36bb9ede4b5522c948a80f045374b] May-19 22:29:38.990 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:38.990 [Task submitter] INFO nextflow.Session - [ef/e0b4da] Submitted process > MapReads (S029-S029-9876T_M4) May-19 22:29:39.252 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; name: MapReads (S011-S011-1234N_M2); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/6d/0c5960fb59f6b6b78d2741af04998b] May-19 22:29:39.256 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:39.256 [Task submitter] INFO nextflow.Session - [d4/50026c] Submitted process > MapReads (S028-S028-9876T_M3) May-19 22:29:39.334 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 114; name: MapReads (S031-S031-1234N_M2); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/e2/e1d97d136c7201fd320b20f9806e0e] May-19 22:29:39.338 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:39.338 [Task submitter] INFO nextflow.Session - [ab/e30808] Submitted process > MapReads (S026-S026-9876T_M1) May-19 22:29:40.711 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 112; name: MapReads (S029-S029-9876T_M4); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/ef/e0b4dad6b3d1c08495b809f6a7cb42] May-19 22:29:40.715 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:40.716 [Task submitter] INFO nextflow.Session - [a7/220b11] Submitted process > MapReads (S020-S020-1234N_M1) May-19 22:29:41.057 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 113; name: MapReads (S030-S030-1234N_M1); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/b0/e5256f2c02b464a8cad3408d00312f] May-19 22:29:41.061 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:41.061 [Task submitter] INFO nextflow.Session - [c7/cccf28] Submitted process > MapReads (S025-S025-1234N_M7) May-19 22:29:41.147 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 111; name: MapReads (S028-S028-9876T_M3); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/d4/50026c27ce2efbf28b04a2895e1962] May-19 22:29:41.211 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 108; name: MapReads (S026-S026-9876T_M1); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/ab/e308089976c833167e1b47b7ba9642] May-19 22:29:42.487 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 103; name: MapReads (S025-S025-1234N_M7); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/c7/cccf2854ae7978b14a3d0f3062291b] May-19 22:29:42.563 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: MapReads (S020-S020-1234N_M1); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/a7/220b11fc661d88a303ac1d32cafc6b] May-19 22:29:42.572 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [af/40ea1b] Cached process > IndexBamFile (S037-S037-9876T) May-19 22:29:42.572 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [1f/62588c] Cached process > IndexBamFile (S013-S013-1234N) May-19 22:29:42.573 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [f3/f90682] Cached process > IndexBamFile (S024-S024-1234N) May-19 22:29:42.575 [Actor Thread 43] INFO nextflow.processor.TaskProcessor - [78/a04437] Cached process > IndexBamFile (S038-S038-9876T) May-19 22:29:42.588 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:42.588 [Task submitter] INFO nextflow.Session - [4d/2264d0] Submitted process > IndexBamFile (S002-S002-1234N) May-19 22:29:42.608 [Actor Thread 13] INFO nextflow.processor.TaskProcessor - [06/018b77] Cached process > IndexBamFile (S035-S035-1234N) May-19 22:29:42.613 [Actor Thread 55] INFO nextflow.processor.TaskProcessor - [74/ef6434] Cached process > IndexBamFile (S034-S034-1234N) May-19 22:29:42.613 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [60/9a0855] Cached process > IndexBamFile (S033-S033-1234N) May-19 22:29:42.615 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [34/c26f81] Cached process > IndexBamFile (S032-S032-1234N) May-19 22:29:42.618 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:42.619 [Task submitter] INFO nextflow.Session - [c7/7d7f1f] Submitted process > IndexBamFile (S001-S001-1234N) May-19 22:29:42.628 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [0f/d23ed5] Cached process > IndexBamFile (S043-S043-1234N) May-19 22:29:42.632 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [11/dd80ad] Cached process > IndexBamFile (S045-S045-1234N) May-19 22:29:42.640 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [e4/9490b5] Cached process > IndexBamFile (S040-S040-1234N) May-19 22:29:42.641 [Actor Thread 48] INFO nextflow.processor.TaskProcessor - [62/7f4757] Cached process > IndexBamFile (S036-S036-9876T) May-19 22:29:42.643 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:42.646 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [3d/7536e0] Cached process > IndexBamFile (S039-S039-9876T) May-19 22:29:42.652 [Task submitter] INFO nextflow.Session - [6c/397db9] Submitted process > IndexBamFile (S007-S007-9876T) May-19 22:29:42.662 [Actor Thread 33] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:42.662 [Actor Thread 16] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:42.662 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [bc/4f7dd7] Cached process > IndexBamFile (S048-S048-9876T) May-19 22:29:42.665 [Actor Thread 61] INFO nextflow.processor.TaskProcessor - [e2/7f2f21] Cached process > IndexBamFile (S049-S049-9876T) May-19 22:29:42.677 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [02/376162] Cached process > IndexBamFile (S042-S042-1234N) May-19 22:29:42.679 [Actor Thread 43] INFO nextflow.processor.TaskProcessor - [1b/e47478] Cached process > IndexBamFile (S044-S044-1234N) May-19 22:29:42.682 [Actor Thread 52] INFO nextflow.processor.TaskProcessor - [1a/70e23c] Cached process > IndexBamFile (S055-S055-1234N) May-19 22:29:42.683 [Actor Thread 47] INFO nextflow.processor.TaskProcessor - [7a/4c7a15] Cached process > IndexBamFile (S046-S046-9876T) May-19 22:29:42.684 [Actor Thread 34] INFO nextflow.processor.TaskProcessor - [8e/7c03c1] Cached process > IndexBamFile (S041-S041-1234N) May-19 22:29:42.694 [Actor Thread 13] INFO nextflow.processor.TaskProcessor - [81/8c91ac] Cached process > IndexBamFile (S051-S051-1234N) May-19 22:29:42.694 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [7f/90d5fe] Cached process > IndexBamFile (S047-S047-9876T) May-19 22:29:42.735 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [82/5cd882] Cached process > IndexBamFile (S058-S058-9876T) May-19 22:29:42.743 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [08/811afc] Cached process > IndexBamFile (S050-S050-1234N) May-19 22:29:42.746 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:42.746 [Actor Thread 49] INFO nextflow.processor.TaskProcessor - [2f/f5a71f] Cached process > IndexBamFile (S057-S057-9876T) May-19 22:29:42.746 [Task submitter] INFO nextflow.Session - [3c/7d5975] Submitted process > IndexBamFile (S004-S004-1234N) May-19 22:29:42.749 [Actor Thread 68] INFO nextflow.processor.TaskProcessor - [7c/0aff38] Cached process > IndexBamFile (S054-S054-1234N) May-19 22:29:42.761 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [cc/b11bb0] Cached process > IndexBamFile (S052-S052-1234N) May-19 22:29:42.807 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:42.810 [Actor Thread 68] INFO nextflow.processor.TaskProcessor - [f0/b3122b] Cached process > IndexBamFile (S062-S062-1234N) May-19 22:29:42.811 [Actor Thread 51] INFO nextflow.processor.TaskProcessor - [3c/fbf8cb] Cached process > IndexBamFile (S053-S053-1234N) May-19 22:29:42.815 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [18/2f489d] Cached process > IndexBamFile (S061-S061-1234N) May-19 22:29:42.816 [Actor Thread 72] INFO nextflow.processor.TaskProcessor - [4a/3f7007] Cached process > IndexBamFile (S064-S064-1234N) May-19 22:29:42.818 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [db/1739f0] Cached process > IndexBamFile (S060-S060-1234N) May-19 22:29:42.830 [Actor Thread 51] INFO nextflow.processor.TaskProcessor - [f8/c8c42b] Cached process > IndexBamFile (S069-S069-9876T) May-19 22:29:42.833 [Actor Thread 49] INFO nextflow.processor.TaskProcessor - [23/fc1c03] Cached process > IndexBamFile (S056-S056-9876T) May-19 22:29:42.846 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [6f/266774] Cached process > IndexBamFile (S059-S059-9876T) May-19 22:29:42.863 [Actor Thread 54] INFO nextflow.processor.TaskProcessor - [26/5967c5] Cached process > IndexBamFile (S068-S068-9876T) May-19 22:29:42.867 [Actor Thread 51] INFO nextflow.processor.TaskProcessor - [59/aec23b] Cached process > IndexBamFile (S063-S063-1234N) May-19 22:29:42.870 [Actor Thread 21] INFO nextflow.processor.TaskProcessor - [05/82ce3b] Cached process > IndexBamFile (S067-S067-9876T) May-19 22:29:42.872 [Actor Thread 49] INFO nextflow.processor.TaskProcessor - [a7/5a03b3] Cached process > IndexBamFile (S066-S066-9876T) May-19 22:29:42.877 [Actor Thread 68] INFO nextflow.processor.TaskProcessor - [13/5b78e2] Cached process > IndexBamFile (S075-S075-1234N) May-19 22:29:42.881 [Actor Thread 54] INFO nextflow.processor.TaskProcessor - [26/669426] Cached process > IndexBamFile (S074-S074-1234N) May-19 22:29:42.885 [Actor Thread 38] INFO nextflow.processor.TaskProcessor - [95/7840b2] Cached process > IndexBamFile (S065-S065-1234N) May-19 22:29:42.889 [Actor Thread 49] INFO nextflow.processor.TaskProcessor - [08/118a03] Cached process > IndexBamFile (S072-S072-1234N) May-19 22:29:42.889 [Actor Thread 21] INFO nextflow.processor.TaskProcessor - [a8/6ab3fe] Cached process > IndexBamFile (S071-S071-1234N) May-19 22:29:42.892 [Actor Thread 51] INFO nextflow.processor.TaskProcessor - [20/26ba5c] Cached process > IndexBamFile (S073-S073-1234N) May-19 22:29:42.895 [Actor Thread 71] INFO nextflow.processor.TaskProcessor - [fa/2bc3aa] Cached process > IndexBamFile (S076-S076-9876T) May-19 22:29:42.900 [Actor Thread 71] INFO nextflow.processor.TaskProcessor - [e7/5d9916] Cached process > IndexBamFile (S083-S083-1234N) May-19 22:29:42.906 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [00/50e54d] Cached process > IndexBamFile (S080-S080-1234N) May-19 22:29:42.907 [Actor Thread 49] INFO nextflow.processor.TaskProcessor - [e2/977b5c] Cached process > IndexBamFile (S084-S084-1234N) May-19 22:29:42.910 [Actor Thread 72] INFO nextflow.processor.TaskProcessor - [3a/6404d7] Cached process > IndexBamFile (S077-S077-9876T) May-19 22:29:42.911 [Actor Thread 51] INFO nextflow.processor.TaskProcessor - [13/aa3a38] Cached process > IndexBamFile (S078-S078-9876T) May-19 22:29:42.914 [Actor Thread 68] INFO nextflow.processor.TaskProcessor - [18/47b911] Cached process > IndexBamFile (S070-S070-1234N) May-19 22:29:42.924 [Actor Thread 72] INFO nextflow.processor.TaskProcessor - [78/fa9bc4] Cached process > IndexBamFile (S091-S091-1234N) May-19 22:29:42.926 [Actor Thread 38] INFO nextflow.processor.TaskProcessor - [50/72e393] Cached process > IndexBamFile (S088-S088-9876T) May-19 22:29:42.933 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [79/d0b322] Cached process > IndexBamFile (S082-S082-1234N) May-19 22:29:42.936 [Actor Thread 54] INFO nextflow.processor.TaskProcessor - [d1/b065ee] Cached process > IndexBamFile (S081-S081-1234N) May-19 22:29:42.939 [Actor Thread 71] INFO nextflow.processor.TaskProcessor - [4f/64240e] Cached process > IndexBamFile (S079-S079-9876T) May-19 22:29:42.941 [Actor Thread 72] INFO nextflow.processor.TaskProcessor - [45/2cf9e1] Cached process > IndexBamFile (S087-S087-9876T) May-19 22:29:42.946 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [04/0c6fec] Cached process > IndexBamFile (S086-S086-9876T) May-19 22:29:42.951 [Actor Thread 49] INFO nextflow.processor.TaskProcessor - [ff/8e4df4] Cached process > IndexBamFile (S097-S097-9876T) May-19 22:29:42.953 [Actor Thread 68] INFO nextflow.processor.TaskProcessor - [41/1ff84b] Cached process > IndexBamFile (S085-S085-1234N) May-19 22:29:42.959 [Actor Thread 69] INFO nextflow.processor.TaskProcessor - [21/68acf6] Cached process > IndexBamFile (S090-S090-1234N) May-19 22:29:42.963 [Actor Thread 49] INFO nextflow.processor.TaskProcessor - [0c/7c12f2] Cached process > IndexBamFile (S093-S093-1234N) May-19 22:29:42.965 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [25/4db1d4] Cached process > IndexBamFile (S092-S092-1234N) May-19 22:29:42.967 [Actor Thread 68] INFO nextflow.processor.TaskProcessor - [41/4b3f28] Cached process > IndexBamFile (S094-S094-1234N) May-19 22:29:42.967 [Actor Thread 83] INFO nextflow.processor.TaskProcessor - [cc/2379d3] Cached process > IndexBamFile (S096-S096-9876T) May-19 22:29:42.967 [Actor Thread 38] INFO nextflow.processor.TaskProcessor - [1e/6e074e] Cached process > IndexBamFile (S089-S089-9876T) May-19 22:29:42.972 [Actor Thread 71] INFO nextflow.processor.TaskProcessor - [00/254bb9] Cached process > IndexBamFile (S095-S095-1234N) May-19 22:29:42.973 [Actor Thread 38] INFO nextflow.processor.TaskProcessor - [44/799fdb] Cached process > IndexBamFile (S099-S099-9876T) May-19 22:29:42.977 [Actor Thread 51] INFO nextflow.processor.TaskProcessor - [35/8141ec] Cached process > IndexBamFile (S098-S098-9876T) May-19 22:29:43.237 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:43.303 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:43.582 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:43.592 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:43.605 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:43.632 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:43.962 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:43.990 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:44.306 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:44.323 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:44.539 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:44.552 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:44.571 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:44.579 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:44.625 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:44.696 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:44.718 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:44.725 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:44.839 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:44.985 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 345; name: IndexBamFile (S002-S002-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/4d/2264d02cb7f983887d2e656cc91378] May-19 22:29:44.993 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:44.993 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:44.995 [Task submitter] INFO nextflow.Session - [73/5c2132] Submitted process > IndexBamFile (S003-S003-1234N) May-19 22:29:45.009 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 347; name: IndexBamFile (S007-S007-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/6c/397db914e6850cc8032fba6b07b1d5] May-19 22:29:45.024 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:45.024 [Task submitter] INFO nextflow.Session - [14/9c10ed] Submitted process > IndexBamFile (S006-S006-9876T) May-19 22:29:45.058 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:45.078 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 344; name: IndexBamFile (S001-S001-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/c7/7d7f1f3c97c986ddbebbf3c5db229c] May-19 22:29:45.086 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:45.086 [Task submitter] INFO nextflow.Session - [7a/ebd571] Submitted process > IndexBamFile (S005-S005-1234N) May-19 22:29:45.163 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 351; name: IndexBamFile (S004-S004-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/3c/7d5975f1cd1fc3b8e6f1b276b61c2a] May-19 22:29:45.167 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:45.168 [Task submitter] INFO nextflow.Session - [c7/5ebec5] Submitted process > IndexBamFile (S000-S000-1234N) May-19 22:29:45.183 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:45.196 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:45.202 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:45.232 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:45.374 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:45.380 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:45.570 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:45.587 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:45.683 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:45.689 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:46.587 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 460; name: IndexBamFile (S003-S003-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/73/5c21326ac4b6fbe0736be630c8f296] May-19 22:29:46.591 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:46.591 [Task submitter] INFO nextflow.Session - [cb/7dcaa0] Submitted process > IndexBamFile (S012-S012-1234N) May-19 22:29:46.622 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:46.651 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:46.691 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:46.699 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 468; name: IndexBamFile (S006-S006-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/14/9c10edbb9a190034ef7951f1c3b550] May-19 22:29:46.704 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:46.718 [Task submitter] INFO nextflow.Session - [03/869d64] Submitted process > IndexBamFile (S008-S008-9876T) May-19 22:29:46.751 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:46.764 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:46.969 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 458; name: IndexBamFile (S005-S005-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/7a/ebd5714848f97d43ed30425440a2d5] May-19 22:29:46.972 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:46.972 [Task submitter] INFO nextflow.Session - [7a/6f56dd] Submitted process > IndexBamFile (S010-S010-1234N) May-19 22:29:47.029 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:47.033 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:47.109 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 461; name: IndexBamFile (S000-S000-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/c7/5ebec50bc3ef74d8ac35da6421526c] May-19 22:29:47.112 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:47.113 [Task submitter] INFO nextflow.Session - [7b/bd137d] Submitted process > IndexBamFile (S018-S018-9876T) May-19 22:29:47.180 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:47.206 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:47.212 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:48.462 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 534; name: IndexBamFile (S012-S012-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/cb/7dcaa07335579756dd1fccda76a381] May-19 22:29:48.465 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:48.465 [Task submitter] INFO nextflow.Session - [67/cd5ef2] Submitted process > IndexBamFile (S009-S009-9876T) May-19 22:29:48.496 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:48.508 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:48.514 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:48.620 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 567; name: IndexBamFile (S008-S008-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/03/869d645ddf0679ccfab6828feffb49] May-19 22:29:48.624 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:48.624 [Task submitter] INFO nextflow.Session - [54/8f7018] Submitted process > IndexBamFile (S016-S016-9876T) May-19 22:29:48.656 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:48.668 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:48.695 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:48.704 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:48.719 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 568; name: IndexBamFile (S010-S010-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/7a/6f56ddec0d35572ff0c71bbc61ef9b] May-19 22:29:48.723 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:48.723 [Task submitter] INFO nextflow.Session - [fa/b86845] Submitted process > IndexBamFile (S017-S017-9876T) May-19 22:29:48.752 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:48.765 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:48.809 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:48.814 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:48.830 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 571; name: IndexBamFile (S018-S018-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/7b/bd137dedc9cce0e5062f0135c06dd5] May-19 22:29:48.834 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:48.834 [Task submitter] INFO nextflow.Session - [ee/831d37] Submitted process > IndexBamFile (S014-S014-1234N) May-19 22:29:48.891 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:48.901 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:48.913 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:48.934 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:48.954 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:50.019 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 600; name: IndexBamFile (S009-S009-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/67/cd5ef2aaa86f5df3cd79b41907fe70] May-19 22:29:50.023 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:50.023 [Task submitter] INFO nextflow.Session - [f6/a8d97f] Submitted process > IndexBamFile (S023-S023-1234N) May-19 22:29:50.050 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:50.070 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:50.081 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:50.234 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 613; name: IndexBamFile (S017-S017-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/fa/b86845b3dabd3c9c95bf0e093a4851] May-19 22:29:50.237 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:50.238 [Task submitter] INFO nextflow.Session - [49/5095e9] Submitted process > IndexBamFile (S022-S022-1234N) May-19 22:29:50.269 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:50.275 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:50.300 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:50.310 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:50.532 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 611; name: IndexBamFile (S016-S016-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/54/8f7018ad1153fefd36743d63522f25] May-19 22:29:50.536 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:50.536 [Task submitter] INFO nextflow.Session - [a5/816558] Submitted process > IndexBamFile (S021-S021-1234N) May-19 22:29:50.590 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:50.606 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:50.732 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 615; name: IndexBamFile (S014-S014-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/ee/831d375e0d4f2f163de10b2b6b7b4c] May-19 22:29:50.737 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:50.737 [Task submitter] INFO nextflow.Session - [38/b5b990] Submitted process > IndexBamFile (S015-S015-1234N) May-19 22:29:50.778 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:50.787 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:51.865 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 616; name: IndexBamFile (S023-S023-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/f6/a8d97f555af771aa6a7e4dc11d2088] May-19 22:29:51.869 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:51.869 [Task submitter] INFO nextflow.Session - [71/cb1e15] Submitted process > IndexBamFile (S019-S019-9876T) May-19 22:29:51.907 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:51.926 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:51.926 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 617; name: IndexBamFile (S022-S022-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/49/5095e99b1c7229849d9cb3ede2f3e3] May-19 22:29:51.930 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:51.930 [Task submitter] INFO nextflow.Session - [cf/1bcbb1] Submitted process > IndexBamFile (S027-S027-9876T) May-19 22:29:51.930 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:51.979 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:51.986 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:52.121 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 624; name: IndexBamFile (S021-S021-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/a5/81655846f8419e1ce280b2d35551de] May-19 22:29:52.125 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:52.125 [Task submitter] INFO nextflow.Session - [66/4887d4] Submitted process > IndexBamFile (S031-S031-1234N) May-19 22:29:52.158 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:52.170 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:52.182 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:52.222 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:52.226 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:52.325 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 625; name: IndexBamFile (S015-S015-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/38/b5b9903965aab6d64e348c072bd50d] May-19 22:29:52.328 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:52.328 [Task submitter] INFO nextflow.Session - [78/88a25b] Submitted process > IndexBamFile (S011-S011-1234N) May-19 22:29:52.373 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:52.387 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:53.600 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 626; name: IndexBamFile (S019-S019-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/71/cb1e1576de5c9affb6bfd95174e3bb] May-19 22:29:53.603 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:53.603 [Task submitter] INFO nextflow.Session - [c7/68351c] Submitted process > IndexBamFile (S029-S029-9876T) May-19 22:29:53.668 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 627; name: IndexBamFile (S027-S027-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/cf/1bcbb1205bcdf65bbcff6eeea92c1e] May-19 22:29:53.675 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:53.675 [Task submitter] INFO nextflow.Session - [f7/094376] Submitted process > IndexBamFile (S030-S030-1234N) May-19 22:29:53.691 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:53.720 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:53.729 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:53.969 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 629; name: IndexBamFile (S031-S031-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/66/4887d47b82176b19e63b6f72f0c72a] May-19 22:29:53.973 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:53.973 [Task submitter] INFO nextflow.Session - [56/f53ac3] Submitted process > IndexBamFile (S028-S028-9876T) May-19 22:29:54.014 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:54.052 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:54.079 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:54.089 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:54.121 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 628; name: IndexBamFile (S011-S011-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/78/88a25bf3d2b4c2c52041c184d410e4] May-19 22:29:54.125 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:54.125 [Task submitter] INFO nextflow.Session - [b6/c112cb] Submitted process > IndexBamFile (S026-S026-9876T) May-19 22:29:54.178 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:54.188 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:54.215 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:54.236 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:55.099 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 631; name: IndexBamFile (S030-S030-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/f7/094376685bcafa3229981c133a1255] May-19 22:29:55.107 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:55.107 [Task submitter] INFO nextflow.Session - [f0/4543d1] Submitted process > IndexBamFile (S025-S025-1234N) May-19 22:29:55.155 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:55.160 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:55.233 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 630; name: IndexBamFile (S029-S029-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/c7/68351c44e00012ce4504c392fdefa3] May-19 22:29:55.236 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-19 22:29:55.236 [Task submitter] INFO nextflow.Session - [74/974472] Submitted process > IndexBamFile (S020-S020-1234N) May-19 22:29:55.285 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:55.292 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:55.364 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 632; name: IndexBamFile (S028-S028-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/56/f53ac3cbcd5ff016446ff30a32b6aa] May-19 22:29:55.434 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:55.447 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:55.469 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:55.478 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:55.549 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 633; name: IndexBamFile (S026-S026-9876T); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/b6/c112cbecebb28ceac4a9e4c842a49a] May-19 22:29:55.590 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:55.600 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:56.509 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 635; name: IndexBamFile (S020-S020-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/74/9744726095220fddbadab780e2af89] May-19 22:29:56.539 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:56.557 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:56.582 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:56.592 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:56.621 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 634; name: IndexBamFile (S025-S025-1234N); status: COMPLETED; exit: 0; error: -; workDir: /home/ssm-user/reprex/work/f0/4543d1b0d8db1a57589aa173f0a41b] May-19 22:29:56.646 [Actor Thread 14] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 100; slices: 1; internal sort time: 0.008 s; external sort time: 0.014 s; total time: 0.022 s May-19 22:29:56.647 [Actor Thread 14] DEBUG nextflow.file.FileCollector - >> temp file exists? false May-19 22:29:56.647 [Actor Thread 14] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /tmp/4c05bccb0fbe43a32ccafd42147c5152.collect-file May-19 22:29:56.672 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta at /home/ssm-user/reprex/work/stage/6e/6932e36d98703471e0c82a2c4d1fab/human_g1k_v37_decoy.small.fasta May-19 22:29:56.673 [Actor Thread 79] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:56.673 [Actor Thread 4] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:56.680 [Actor Thread 14] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/4c05bccb0fbe43a32ccafd42147c5152.collect-file May-19 22:29:56.685 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/dbsnp_138.b37.small.vcf.gz at /home/ssm-user/reprex/work/stage/a3/6a4eb8ae22a8dcaefc7919ba21bfdb/dbsnp_138.b37.small.vcf.gz May-19 22:29:56.686 [Actor Thread 22] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:56.687 [Actor Thread 40] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:56.688 [Actor Thread 84] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:56.688 [Actor Thread 4] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null May-19 22:29:56.688 [main] DEBUG nextflow.Session - Session await > all process finished May-19 22:29:56.692 [Actor Thread 14] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-15926285344116679497 May-19 22:29:56.718 [Actor Thread 38] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 100; slices: 1; internal sort time: 0.086 s; external sort time: 0.007 s; total time: 0.093 s May-19 22:29:56.718 [Actor Thread 38] DEBUG nextflow.file.FileCollector - >> temp file exists? false May-19 22:29:56.718 [Actor Thread 38] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /tmp/c5f3cb07c895452ff793b5a0fdf7ea22.collect-file May-19 22:29:56.722 [main] DEBUG nextflow.Session - Session await > all barriers passed May-19 22:29:56.728 [Actor Thread 38] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /tmp/c5f3cb07c895452ff793b5a0fdf7ea22.collect-file May-19 22:29:56.733 [Actor Thread 38] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-10984210094331238341 May-19 22:29:56.874 [main] INFO nextflow.Nextflow - -[nf-core/sarek] Pipeline completed successfully- May-19 22:29:56.879 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=60; failedCount=0; ignoredCount=0; cachedCount=144; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=5.1s; failedDuration=0ms; cachedDuration=19.7s;loadCpus=0; loadMemory=0; peakRunning=4; peakCpus=8; peakMemory=24 GB; ] May-19 22:29:56.879 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file May-19 22:29:56.881 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report May-19 22:29:57.004 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":{"mean":20.7,"min":20.7,"q1":20.7,"q2":20.7,"q3":20.7,"max":20.7,"minLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)"},"process":"BuildFastaFai","mem":null,"memUsage":null,"timeUsage":null,"vmem":null,"reads":{"mean":863450,"min":863450,"q1":863450,"q2":863450,"q3":863450,"max":863450,"minLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)"},"cpu":{"mean":41.4,"min":41.4,"q1":41.4,"q2":41.4,"q3":41.4,"max":41.4,"minLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)"},"time":{"mean":36,"min":36,"q1":36,"q2":36,"q3":36,"max":36,"minLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)"},"writes":{"mean":311,"min":311,"q1":311,"q2":311,"q3":311,"max":311,"minLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildFastaFai (human_g1k_v37_decoy.small.fasta)"}},{"cpuUsage":{"mean":41.1,"min":41.1,"q1":41.1,"q2":41.1,"q3":41.1,"max":41.1,"minLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)"},"process":"BuildBWAindexes","mem":{"mean":14372864,"min":14372864,"q1":14372864,"q2":14372864,"q3":14372864,"max":14372864,"minLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)"},"memUsage":{"mean":0.22,"min":0.22,"q1":0.22,"q2":0.22,"q3":0.22,"max":0.22,"minLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)"},"timeUsage":null,"vmem":{"mean":18702336,"min":18702336,"q1":18702336,"q2":18702336,"q3":18702336,"max":18702336,"minLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)"},"reads":{"mean":3290765,"min":3290765,"q1":3290765,"q2":3290765,"q3":3290765,"max":3290765,"minLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)"},"cpu":{"mean":82.2,"min":82.2,"q1":82.2,"q2":82.2,"q3":82.2,"max":82.2,"minLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)"},"time":{"mean":560,"min":560,"q1":560,"q2":560,"q3":560,"max":560,"minLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)"},"writes":{"mean":2215441,"min":2215441,"q1":2215441,"q2":2215441,"q3":2215441,"max":2215441,"minLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildBWAindexes (human_g1k_v37_decoy.small.fasta)"}},{"cpuUsage":{"mean":75.95,"min":75.95,"q1":75.95,"q2":75.95,"q3":75.95,"max":75.95,"minLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildDict (human_g1k_v37_decoy.small.fasta)"},"process":"BuildDict","mem":{"mean":207085568,"min":207085568,"q1":207085568,"q2":207085568,"q3":207085568,"max":207085568,"minLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildDict (human_g1k_v37_decoy.small.fasta)"},"memUsage":{"mean":3.21,"min":3.21,"q1":3.21,"q2":3.21,"q3":3.21,"max":3.21,"minLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildDict (human_g1k_v37_decoy.small.fasta)"},"timeUsage":{"mean":0.01,"min":0.01,"q1":0.01,"q2":0.01,"q3":0.01,"max":0.01,"minLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildDict (human_g1k_v37_decoy.small.fasta)"},"vmem":{"mean":8896663552,"min":8896663552,"q1":8896663552,"q2":8896663552,"q3":8896663552,"max":8896663552,"minLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildDict (human_g1k_v37_decoy.small.fasta)"},"reads":{"mean":33107034,"min":33107034,"q1":33107034,"q2":33107034,"q3":33107034,"max":33107034,"minLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildDict (human_g1k_v37_decoy.small.fasta)"},"cpu":{"mean":151.9,"min":151.9,"q1":151.9,"q2":151.9,"q3":151.9,"max":151.9,"minLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildDict (human_g1k_v37_decoy.small.fasta)"},"time":{"mean":4688,"min":4688,"q1":4688,"q2":4688,"q3":4688,"max":4688,"minLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildDict (human_g1k_v37_decoy.small.fasta)"},"writes":{"mean":635273,"min":635273,"q1":635273,"q2":635273,"q3":635273,"max":635273,"minLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","maxLabel":"BuildDict (human_g1k_v37_decoy.small.fasta)","q1Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q2Label":"BuildDict (human_g1k_v37_decoy.small.fasta)","q3Label":"BuildDict (human_g1k_v37_decoy.small.fasta)"}},{"cpuUsage":{"mean":32,"min":32,"q1":32,"q2":32,"q3":32,"max":32,"minLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","maxLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q1Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q2Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q3Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)"},"process":"BuildDbsnpIndex","mem":{"mean":3211264,"min":3211264,"q1":3211264,"q2":3211264,"q3":3211264,"max":3211264,"minLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","maxLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q1Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q2Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q3Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)"},"memUsage":{"mean":0.05,"min":0.05,"q1":0.05,"q2":0.05,"q3":0.05,"max":0.05,"minLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","maxLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q1Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q2Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q3Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)"},"timeUsage":null,"vmem":{"mean":5636096,"min":5636096,"q1":5636096,"q2":5636096,"q3":5636096,"max":5636096,"minLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","maxLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q1Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q2Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q3Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)"},"reads":{"mean":371889,"min":371889,"q1":371889,"q2":371889,"q3":371889,"max":371889,"minLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","maxLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q1Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q2Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q3Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)"},"cpu":{"mean":64,"min":64,"q1":64,"q2":64,"q3":64,"max":64,"minLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","maxLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q1Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q2Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q3Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)"},"time":{"mean":48,"min":48,"q1":48,"q2":48,"q3":48,"max":48,"minLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","maxLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q1Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q2Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q3Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)"},"writes":{"mean":777,"min":777,"q1":777,"q2":777,"q3":777,"max":777,"minLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","maxLabel":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q1Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q2Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)","q3Label":"BuildDbsnpIndex (dbsnp_138.b37.small.vcf.gz)"}},{"cpuUsage":{"mean":43.04,"min":12.1,"q1":32,"q2":36.35,"q3":59.96,"max":73.25,"minLabel":"MapReads (S002-S002-1234N_M4)","maxLabel":"MapReads (S079-S079-9876T_M4)","q1Label":"MapReads (S004-S004-1234N_M6)","q2Label":"MapReads (S082-S082-1234N_M4)","q3Label":"MapReads (S067-S067-9876T_M2)"},"process":"MapReads","mem":{"mean":6360391.68,"min":3141632,"q1":3268608,"q2":3330048,"q3":11385856,"max":14974976,"minLabel":"MapReads (S055-S055-1234N_M7)","maxLabel":"MapReads (S009-S009-9876T_M4)","q1Label":"MapReads (S072-S072-1234N_M4)","q2Label":"MapReads (S005-S005-1234N_M7)","q3Label":"MapReads (S077-S077-9876T_M2)"},"memUsage":{"mean":0.1,"min":0.05,"q1":0.05,"q2":0.05,"q3":0.18,"max":0.23,"minLabel":"MapReads (S055-S055-1234N_M7)","maxLabel":"MapReads (S009-S009-9876T_M4)","q1Label":"MapReads (S072-S072-1234N_M4)","q2Label":"MapReads (S005-S005-1234N_M7)","q3Label":"MapReads (S077-S077-9876T_M2)"},"timeUsage":null,"vmem":{"mean":1683899351.04,"min":5636096,"q1":5636096,"q2":5636096,"q3":4732095488,"max":4926238720,"minLabel":"MapReads (S001-S001-1234N_M2)","maxLabel":"MapReads (S076-S076-9876T_M1)","q1Label":"MapReads (S064-S064-1234N_M6)","q2Label":"MapReads (S094-S094-1234N_M6)","q3Label":"MapReads (S087-S087-9876T_M2)"},"reads":{"mean":1775256.56,"min":1490194,"q1":1523784,"q2":1545518,"q3":2125643,"max":2210716,"minLabel":"MapReads (S041-S041-1234N_M2)","maxLabel":"MapReads (S029-S029-9876T_M4)","q1Label":"MapReads (S072-S072-1234N_M4)","q2Label":"MapReads (S014-S014-1234N_M6)","q3Label":"MapReads (S088-S088-9876T_M3)"},"cpu":{"mean":86.09,"min":24.2,"q1":64,"q2":72.7,"q3":119.93,"max":146.5,"minLabel":"MapReads (S002-S002-1234N_M4)","maxLabel":"MapReads (S079-S079-9876T_M4)","q1Label":"MapReads (S004-S004-1234N_M6)","q2Label":"MapReads (S082-S082-1234N_M4)","q3Label":"MapReads (S067-S067-9876T_M2)"},"time":{"mean":61.04,"min":21,"q1":36,"q2":45,"q3":84.5,"max":179,"minLabel":"MapReads (S071-S071-1234N_M2)","maxLabel":"MapReads (S009-S009-9876T_M4)","q1Label":"MapReads (S042-S042-1234N_M4)","q2Label":"MapReads (S095-S095-1234N_M7)","q3Label":"MapReads (S097-S097-9876T_M2)"},"writes":{"mean":324931.95,"min":29435,"q1":64067,"q2":85810.5,"q3":689146.25,"max":776832,"minLabel":"MapReads (S031-S031-1234N_M2)","maxLabel":"MapReads (S089-S089-9876T_M4)","q1Label":"MapReads (S072-S072-1234N_M4)","q2Label":"MapReads (S004-S004-1234N_M6)","q3Label":"MapReads (S088-S088-9876T_M3)"}},{"cpuUsage":{"mean":39.92,"min":9.1,"q1":30.75,"q2":34.8,"q3":50,"max":80,"minLabel":"IndexBamFile (S004-S004-1234N)","maxLabel":"IndexBamFile (S022-S022-1234N)","q1Label":"IndexBamFile (S066-S066-9876T)","q2Label":"IndexBamFile (S050-S050-1234N)","q3Label":"IndexBamFile (S013-S013-1234N)"},"process":"IndexBamFile","mem":{"mean":163840,"min":0,"q1":0,"q2":0,"q3":0,"max":3350528,"minLabel":"IndexBamFile (S013-S013-1234N)","maxLabel":"IndexBamFile (S029-S029-9876T)","q1Label":"IndexBamFile (S052-S052-1234N)","q2Label":"IndexBamFile (S078-S078-9876T)","q3Label":"IndexBamFile (S000-S000-1234N)"},"memUsage":{"mean":0.05,"min":0.05,"q1":0.05,"q2":0.05,"q3":0.05,"max":0.05,"minLabel":"IndexBamFile (S016-S016-9876T)","maxLabel":"IndexBamFile (S029-S029-9876T)","q1Label":"IndexBamFile (S081-S081-1234N)","q2Label":"IndexBamFile (S037-S037-9876T)","q3Label":"IndexBamFile (S066-S066-9876T)"},"timeUsage":null,"vmem":{"mean":281804.8,"min":0,"q1":0,"q2":0,"q3":0,"max":5636096,"minLabel":"IndexBamFile (S013-S013-1234N)","maxLabel":"IndexBamFile (S029-S029-9876T)","q1Label":"IndexBamFile (S052-S052-1234N)","q2Label":"IndexBamFile (S078-S078-9876T)","q3Label":"IndexBamFile (S000-S000-1234N)"},"reads":{"mean":110084.79,"min":55570,"q1":63086,"q2":66599,"q3":177009,"max":190314,"minLabel":"IndexBamFile (S031-S031-1234N)","maxLabel":"IndexBamFile (S089-S089-9876T)","q1Label":"IndexBamFile (S052-S052-1234N)","q2Label":"IndexBamFile (S004-S004-1234N)","q3Label":"IndexBamFile (S038-S038-9876T)"},"cpu":{"mean":79.85,"min":18.2,"q1":61.5,"q2":69.6,"q3":100,"max":160,"minLabel":"IndexBamFile (S004-S004-1234N)","maxLabel":"IndexBamFile (S022-S022-1234N)","q1Label":"IndexBamFile (S066-S066-9876T)","q2Label":"IndexBamFile (S050-S050-1234N)","q3Label":"IndexBamFile (S013-S013-1234N)"},"time":{"mean":9.53,"min":6,"q1":8,"q2":9,"q3":10,"max":28,"minLabel":"IndexBamFile (S020-S020-1234N)","maxLabel":"IndexBamFile (S004-S004-1234N)","q1Label":"IndexBamFile (S035-S035-1234N)","q2Label":"IndexBamFile (S050-S050-1234N)","q3Label":"IndexBamFile (S088-S088-9876T)"},"writes":{"mean":394.26,"min":394,"q1":394,"q2":394,"q3":395,"max":395,"minLabel":"IndexBamFile (S024-S024-1234N)","maxLabel":"IndexBamFile (S028-S028-9876T)","q1Label":"IndexBamFile (S064-S064-1234N)","q2Label":"IndexBamFile (S087-S087-9876T)","q3Label":"IndexBamFile (S013-S013-1234N)"}}] May-19 22:29:57.731 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline May-19 22:29:57.918 [main] WARN nextflow.dag.GraphvizRenderer - To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. May-19 22:29:58.311 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done May-19 22:29:58.311 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-tower@1.4.0' May-19 22:29:58.312 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-tower May-19 22:29:58.339 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye