Jun-07 16:38:54.136 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/eager -r dev --pairedEnd --reads 'data/*pass_{1,2}.fastq.gz' --fasta reference/Enterobacteria_phage_lambda.fasta --bwa_index reference/Enterobacteria_phage_lambda.fasta --fasta_index reference/Enterobacteria_phage_lambda.fasta.fai --outdir output_devIndex/ --clip_readlength 35 --clip_min_read_quality 0 --clip_min_adap_overlap 3 --bwaalnn 0.01 --bwaalnl 16500 --bam_mapping_quality_threshold 30 --max_cpus 5 --max_time 8.h -name IndexTest_devIndex_Run2 Jun-07 16:38:54.381 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.01.0 Jun-07 16:38:55.792 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/keaton/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git Jun-07 16:38:55.809 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/keaton/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git Jun-07 16:38:55.942 [main] WARN org.eclipse.jgit.util.FS - Exception caught during execution of command '[git, config, --system, --edit]' in '/home/keaton/bin', return code '128', error message 'fatal: Invalid path '/home/keaton/etc': No such file or directory ' Jun-07 16:38:56.323 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/keaton/.nextflow/assets/nf-core/eager/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/eager.git Jun-07 16:38:56.324 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/eager` [IndexTest_devIndex_Run2] - revision: 59fbcc1007 [dev] Jun-07 16:38:56.791 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/keaton/.nextflow/assets/nf-core/eager/nextflow.config Jun-07 16:38:56.793 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/keaton/.nextflow/assets/nf-core/eager/nextflow.config Jun-07 16:38:56.808 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` Jun-07 16:38:57.522 [main] DEBUG nextflow.Session - Session uuid: c84d6e98-b7d3-4885-94f0-583204c4ed54 Jun-07 16:38:57.522 [main] DEBUG nextflow.Session - Run name: IndexTest_devIndex_Run2 Jun-07 16:38:57.523 [main] DEBUG nextflow.Session - Executor pool size: 48 Jun-07 16:38:57.541 [main] DEBUG nextflow.cli.CmdRun - Version: 19.01.0 build 5050 Modified: 22-01-2019 11:19 UTC (06:19 EDT) System: Linux 2.6.32-754.3.5.el6.x86_64 Runtime: Groovy 2.5.5 on OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12 Encoding: UTF-8 (UTF-8) Process: 12085@info113 [10.10.10.113] CPUs: 48 - Mem: 252.4 GB (93.3 GB) - Swap: 1 GB (562.6 MB) Jun-07 16:38:57.572 [main] DEBUG nextflow.Session - Work-dir: /home/keaton/Projects/EAGER/IndexTest/work [nfs] Jun-07 16:38:57.871 [main] DEBUG nextflow.Session - Session start invoked Jun-07 16:38:57.879 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start Jun-07 16:38:57.880 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/keaton/Projects/EAGER/IndexTest/output_devIndex/pipeline_info/execution_trace.txt Jun-07 16:38:57.886 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing Jun-07 16:38:59.147 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jun-07 16:38:59.410 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: data/; pattern: *pass_{1,2}.fastq.gz; options: [:] Jun-07 16:38:59.440 [main] INFO nextflow.Nextflow - ---------------------------------------------------- ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/eager v2.0.7dev ---------------------------------------------------- Jun-07 16:38:59.448 [main] INFO nextflow.Nextflow - Pipeline Name : nf-core/eager Pipeline Version : 2.0.7dev Run Name : IndexTest_devIndex_Run2 Reads : data/*pass_{1,2}.fastq.gz Fasta Ref : reference/Enterobacteria_phage_lambda.fasta BAM Index Type : CSI BWA Index : reference/Enterobacteria_phage_lambda.fasta Data Type : Paired-End Skip Collapsing : No Skip Trimming : No Output stripped fastq: No Max Memory : 128 GB Max CPUs : 5 Max Time : 8.h Output dir : output_devIndex/ Working dir : /home/keaton/Projects/EAGER/IndexTest/work Container Engine : null Current home : /home/keaton Current user : keaton Current path : /home/keaton/Projects/EAGER/IndexTest Script dir : /home/keaton/.nextflow/assets/nf-core/eager Config Profile : standard Jun-07 16:38:59.448 [main] INFO nextflow.Nextflow - ---------------------------------------------------- Jun-07 16:38:59.564 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.565 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.577 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.581 [main] INFO nextflow.executor.Executor - [warm up] executor > local Jun-07 16:38:59.588 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=48; memory=252.4 GB; capacity=48; pollInterval=100ms; dumpInterval=5m Jun-07 16:38:59.595 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor Jun-07 16:38:59.596 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Jun-07 16:38:59.600 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local Jun-07 16:38:59.658 [main] DEBUG nextflow.Session - >>> barrier register (process: makeFastaIndex) Jun-07 16:38:59.662 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeFastaIndex -- maxForks: 48 Jun-07 16:38:59.711 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:makeSeqDict` matches process makeSeqDict Jun-07 16:38:59.718 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.718 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.718 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.720 [main] DEBUG nextflow.Session - >>> barrier register (process: makeSeqDict) Jun-07 16:38:59.721 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeSeqDict -- maxForks: 48 Jun-07 16:38:59.763 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:convertBam` matches process convertBam Jun-07 16:38:59.766 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.767 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.767 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.769 [main] DEBUG nextflow.Session - >>> barrier register (process: convertBam) Jun-07 16:38:59.769 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > convertBam -- maxForks: 48 Jun-07 16:38:59.792 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: convertBam) Jun-07 16:38:59.805 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: makeFastaIndex) Jun-07 16:38:59.814 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:fastqc` matches process fastqc Jun-07 16:38:59.818 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.818 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.819 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.822 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc) Jun-07 16:38:59.824 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 48 Jun-07 16:38:59.843 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.843 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.844 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.845 [main] DEBUG nextflow.Session - >>> barrier register (process: fastp) Jun-07 16:38:59.845 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastp -- maxForks: 48 Jun-07 16:38:59.866 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.867 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.867 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.868 [main] DEBUG nextflow.Session - >>> barrier register (process: adapter_removal) Jun-07 16:38:59.869 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > adapter_removal -- maxForks: 48 Jun-07 16:38:59.869 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: fastp) Jun-07 16:38:59.888 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.888 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.888 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.890 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc_after_clipping) Jun-07 16:38:59.893 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc_after_clipping -- maxForks: 48 Jun-07 16:38:59.918 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:bwa` matches process bwa Jun-07 16:38:59.920 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.920 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.920 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.924 [main] DEBUG nextflow.Session - >>> barrier register (process: bwa) Jun-07 16:38:59.925 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bwa -- maxForks: 48 Jun-07 16:38:59.938 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.939 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.939 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.941 [main] DEBUG nextflow.Session - >>> barrier register (process: circulargenerator) Jun-07 16:38:59.942 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > circulargenerator -- maxForks: 48 Jun-07 16:38:59.951 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: circulargenerator) Jun-07 16:38:59.958 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:38:59.959 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:38:59.959 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:38:59.961 [main] DEBUG nextflow.Session - >>> barrier register (process: circularmapper) Jun-07 16:38:59.961 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > circularmapper -- maxForks: 48 Jun-07 16:38:59.970 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: circularmapper) Jun-07 16:39:00.137 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:bwamem` matches process bwamem Jun-07 16:39:00.138 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.138 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.139 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.141 [main] DEBUG nextflow.Session - >>> barrier register (process: bwamem) Jun-07 16:39:00.142 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bwamem -- maxForks: 48 Jun-07 16:39:00.158 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.159 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.159 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.160 [main] DEBUG nextflow.Session - >>> barrier register (process: samtools_idxstats) Jun-07 16:39:00.161 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > samtools_idxstats -- maxForks: 48 Jun-07 16:39:00.172 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.173 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.173 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.174 [main] DEBUG nextflow.Session - >>> barrier register (process: samtools_filter) Jun-07 16:39:00.174 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > samtools_filter -- maxForks: 48 Jun-07 16:39:00.188 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:strip_input_fastq` matches process strip_input_fastq Jun-07 16:39:00.189 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.189 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.190 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:00.190 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.191 [main] DEBUG nextflow.Session - >>> barrier register (process: strip_input_fastq) Jun-07 16:39:00.191 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > strip_input_fastq -- maxForks: 48 Jun-07 16:39:00.199 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.200 [Task submitter] INFO nextflow.Session - [3d/68dca2] Submitted process > makeSeqDict (Enterobacteria_phage_lambda.fasta) Jun-07 16:39:00.200 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.200 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.201 [main] DEBUG nextflow.Session - >>> barrier register (process: dedup) Jun-07 16:39:00.202 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dedup -- maxForks: 48 Jun-07 16:39:00.210 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:preseq` matches process preseq Jun-07 16:39:00.212 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.212 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.214 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.217 [main] DEBUG nextflow.Session - >>> barrier register (process: preseq) Jun-07 16:39:00.218 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 48 Jun-07 16:39:00.233 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:damageprofiler` matches process damageprofiler Jun-07 16:39:00.233 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:00.234 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.234 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.234 [Task submitter] INFO nextflow.Session - [e1/fd8ece] Submitted process > fastqc (TestData01) Jun-07 16:39:00.234 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.236 [main] DEBUG nextflow.Session - >>> barrier register (process: damageprofiler) Jun-07 16:39:00.236 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > damageprofiler -- maxForks: 48 Jun-07 16:39:00.244 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:qualimap` matches process qualimap Jun-07 16:39:00.245 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.245 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.246 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.247 [main] DEBUG nextflow.Session - >>> barrier register (process: qualimap) Jun-07 16:39:00.247 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > qualimap -- maxForks: 48 Jun-07 16:39:00.252 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:00.253 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:markDup` matches process markDup Jun-07 16:39:00.253 [Task submitter] INFO nextflow.Session - [15/f40e74] Submitted process > fastqc (TestData02) Jun-07 16:39:00.254 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.254 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.254 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.255 [main] DEBUG nextflow.Session - >>> barrier register (process: markDup) Jun-07 16:39:00.255 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > markDup -- maxForks: 48 Jun-07 16:39:00.268 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.268 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.269 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.270 [main] DEBUG nextflow.Session - >>> barrier register (process: pmdtools) Jun-07 16:39:00.270 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > pmdtools -- maxForks: 48 Jun-07 16:39:00.271 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:00.272 [Task submitter] INFO nextflow.Session - [cd/de2157] Submitted process > fastqc (TestData03) Jun-07 16:39:00.276 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:bam_trim` matches process bam_trim Jun-07 16:39:00.277 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.277 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.277 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.278 [main] DEBUG nextflow.Session - >>> barrier register (process: bam_trim) Jun-07 16:39:00.279 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bam_trim -- maxForks: 48 Jun-07 16:39:00.283 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.283 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.284 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.285 [main] DEBUG nextflow.Session - >>> barrier register (process: output_documentation) Jun-07 16:39:00.285 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 48 Jun-07 16:39:00.286 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:00.286 [Task submitter] INFO nextflow.Session - [95/cf6b08] Submitted process > adapter_removal (TestData02) Jun-07 16:39:00.288 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:get_software_versions` matches process get_software_versions Jun-07 16:39:00.290 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.290 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.290 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.291 [main] DEBUG nextflow.Session - >>> barrier register (process: get_software_versions) Jun-07 16:39:00.291 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 48 Jun-07 16:39:00.300 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:00.300 [Task submitter] INFO nextflow.Session - [d5/0e17b6] Submitted process > adapter_removal (TestData03) Jun-07 16:39:00.312 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:00.313 [Task submitter] INFO nextflow.Session - [af/5e7530] Submitted process > adapter_removal (TestData01) Jun-07 16:39:00.326 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:00.327 [Task submitter] INFO nextflow.Session - [2f/cb712f] Submitted process > output_documentation Jun-07 16:39:00.338 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:multiqc` matches process multiqc Jun-07 16:39:00.340 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-07 16:39:00.340 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-07 16:39:00.340 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-07 16:39:00.341 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc) Jun-07 16:39:00.342 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 48 Jun-07 16:39:00.348 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Jun-07 16:39:00.348 [main] DEBUG nextflow.Session - Session await Jun-07 16:39:06.259 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: makeSeqDict (Enterobacteria_phage_lambda.fasta); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/3d/68dca2ccced5de2a1ddd80f4acfea3] Jun-07 16:39:06.297 [Actor Thread 13] DEBUG nextflow.Session - <<< barrier arrive (process: makeSeqDict) Jun-07 16:39:06.434 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: output_documentation; status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/2f/cb712f1cd23c272ed4bcd9ed66a0b3] Jun-07 16:39:06.438 [Actor Thread 13] DEBUG nextflow.Session - <<< barrier arrive (process: output_documentation) Jun-07 16:39:27.047 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: fastqc (TestData01); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/e1/fd8ece2eabe226d763a415d14011bb] Jun-07 16:39:27.403 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: fastqc (TestData02); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/15/f40e740f25d102cfaf588f3d5695a9] Jun-07 16:39:27.415 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: fastqc (TestData03); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/cd/de21573500eeda03a120b39be3b30a] Jun-07 16:39:27.422 [Actor Thread 13] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc) Jun-07 16:39:52.876 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: adapter_removal (TestData02); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/95/cf6b08a386916c84ca091cf47f689a] Jun-07 16:39:52.902 [Actor Thread 21] DEBUG nextflow.Session - <<< barrier arrive (process: bwamem) Jun-07 16:39:52.933 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:52.933 [Task submitter] INFO nextflow.Session - [71/60e771] Submitted process > fastqc_after_clipping (TestData02.pass_1.fastq) Jun-07 16:39:53.223 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: adapter_removal (TestData03); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/d5/0e17b658c6a988ba3bdf0639bbe2d4] Jun-07 16:39:53.229 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:53.229 [Task submitter] INFO nextflow.Session - [ed/b567d4] Submitted process > bwa (TestData02.pass_1.fastq) Jun-07 16:39:53.240 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: adapter_removal (TestData01); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/af/5e75305cfe0f9ce7ccc4369bbca52b] Jun-07 16:39:53.251 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:53.252 [Task submitter] INFO nextflow.Session - [8e/be6de0] Submitted process > fastqc_after_clipping (TestData03.pass_1.fastq) Jun-07 16:39:53.254 [Actor Thread 21] DEBUG nextflow.Session - <<< barrier arrive (process: adapter_removal) Jun-07 16:39:53.266 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:39:53.266 [Task submitter] INFO nextflow.Session - [66/dcb279] Submitted process > fastqc_after_clipping (TestData01.pass_1.fastq) Jun-07 16:40:10.027 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: fastqc_after_clipping (TestData03.pass_1.fastq); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/8e/be6de05c7a1e72b375cb01a27d07fc] Jun-07 16:40:10.071 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: fastqc_after_clipping (TestData01.pass_1.fastq); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/66/dcb2796e6940ef50429c8e9c80f829] Jun-07 16:40:10.172 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: fastqc_after_clipping (TestData02.pass_1.fastq); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/71/60e7711c930479ab3850f0179bc426] Jun-07 16:40:10.177 [Actor Thread 23] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc_after_clipping) Jun-07 16:41:32.564 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: bwa (TestData02.pass_1.fastq); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/ed/b567d4e6f17923d9970c5d125bd34f] Jun-07 16:41:32.580 [Actor Thread 31] DEBUG nextflow.Session - <<< barrier arrive (process: bwa) Jun-07 16:41:32.584 [Actor Thread 36] DEBUG nextflow.Session - <<< barrier arrive (process: strip_input_fastq) Jun-07 16:41:32.593 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:41:32.593 [Task submitter] INFO nextflow.Session - [cb/d83538] Submitted process > samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted) Jun-07 16:41:32.617 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:41:32.618 [Task submitter] INFO nextflow.Session - [85/7f3264] Submitted process > damageprofiler (TestData02.pass_1.fastq.combined.fq.sorted) Jun-07 16:41:32.835 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:41:32.835 [Task submitter] INFO nextflow.Session - [a1/61e362] Submitted process > samtools_filter (TestData02.pass_1.fastq.combined.fq.sorted.bam) Jun-07 16:41:38.601 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/cb/d835389d1ec39e9d443f01c25e5909] Jun-07 16:41:38.608 [Actor Thread 23] DEBUG nextflow.Session - <<< barrier arrive (process: samtools_idxstats) Jun-07 16:41:38.689 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: samtools_filter (TestData02.pass_1.fastq.combined.fq.sorted.bam); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/a1/61e362468ea6aa2dd8bef8e8503c6d] Jun-07 16:41:38.810 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process samtools_filter > Skipping output binding because one or more optional files are missing: fileoutparam<1> Jun-07 16:41:38.811 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process samtools_filter > Skipping output binding because one or more optional files are missing: fileoutparam<2> Jun-07 16:41:38.814 [Actor Thread 31] DEBUG nextflow.Session - <<< barrier arrive (process: samtools_filter) Jun-07 16:41:38.816 [Actor Thread 30] DEBUG nextflow.Session - <<< barrier arrive (process: markDup) Jun-07 16:41:39.078 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:41:39.079 [Task submitter] INFO nextflow.Session - [8b/109241] Submitted process > qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered) Jun-07 16:41:39.090 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:41:39.091 [Task submitter] INFO nextflow.Session - [55/6b513b] Submitted process > dedup (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered) Jun-07 16:41:54.536 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: damageprofiler (TestData02.pass_1.fastq.combined.fq.sorted); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/85/7f3264357b1fd2faabf94b909ac8e5] Jun-07 16:41:54.546 [Actor Thread 23] DEBUG nextflow.Session - <<< barrier arrive (process: damageprofiler) Jun-07 16:41:54.580 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:41:54.581 [Task submitter] INFO nextflow.Session - [8b/c327d5] Submitted process > get_software_versions (1) Jun-07 16:41:55.497 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/8b/1092415aa2be0406b6eee3b8ed0850] Jun-07 16:41:55.507 [Actor Thread 40] DEBUG nextflow.Session - <<< barrier arrive (process: qualimap) Jun-07 16:42:05.611 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: get_software_versions (1); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/8b/c327d5a6769330a057b69d0530625e] Jun-07 16:42:05.613 [Actor Thread 40] DEBUG nextflow.Session - <<< barrier arrive (process: get_software_versions) Jun-07 16:42:47.258 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: dedup (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/55/6b513bcd6d706ca25c2f409c5e277c] Jun-07 16:42:47.270 [Actor Thread 42] DEBUG nextflow.Session - <<< barrier arrive (process: dedup) Jun-07 16:42:47.272 [Actor Thread 47] DEBUG nextflow.Session - <<< barrier arrive (process: bam_trim) Jun-07 16:42:47.272 [Actor Thread 42] DEBUG nextflow.Session - <<< barrier arrive (process: pmdtools) Jun-07 16:42:47.307 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:42:47.308 [Task submitter] INFO nextflow.Session - [e9/38c8dd] Submitted process > preseq (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered) Jun-07 16:42:47.746 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: preseq (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/e9/38c8ddd604928c14d3a5c45e396355] Jun-07 16:42:47.750 [Actor Thread 52] DEBUG nextflow.Session - <<< barrier arrive (process: preseq) Jun-07 16:42:47.787 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-07 16:42:47.788 [Task submitter] INFO nextflow.Session - [15/2bc362] Submitted process > multiqc Jun-07 16:42:58.924 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: multiqc; status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/IndexTest/work/15/2bc36204e3d27fcb872fe09c7be094] Jun-07 16:42:58.938 [Actor Thread 52] DEBUG nextflow.Session - <<< barrier arrive (process: multiqc) Jun-07 16:42:58.939 [main] DEBUG nextflow.Session - Session await > all process finished Jun-07 16:42:58.941 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) Jun-07 16:42:58.941 [main] DEBUG nextflow.Session - Session await > all barriers passed Jun-07 16:42:59.614 [main] INFO nextflow.Nextflow - Warning, pipeline completed, but with errored process(es)  Jun-07 16:42:59.615 [main] INFO nextflow.Nextflow - Number of ignored errored process(es) : 0  Jun-07 16:42:59.615 [main] INFO nextflow.Nextflow - Number of successfully ran process(es) : 20  Jun-07 16:42:59.615 [main] INFO nextflow.Nextflow - [nf-core/eager] Pipeline completed successfully Jun-07 16:42:59.621 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=20; failedCount=0; ignoredCount=0; cachedCount=0; succeedDuration=15m 27s; failedDuration=0ms; cachedDuration=0ms] Jun-07 16:42:59.621 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Jun-07 16:42:59.625 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Jun-07 16:42:59.741 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: 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(TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","maxLabel":"qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","q1Label":"qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","q2Label":"qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","q3Label":"qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)"},"reads":null,"writes":{"mean":32768,"min":32768,"q1":32768,"q2":32768,"q3":32768,"max":32768,"minLabel":"qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","maxLabel":"qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","q1Label":"qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","q2Label":"qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","q3Label":"qualimap (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)"},"cpuUsage":{"mean":104.86,"min":104.86,"q1":104.86,"q2":104.86,"q3":104.86,"max":104.86,"minLabel":"qualimap 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(TestData03)"},"memUsage":{"mean":1.54,"min":1.54,"q1":1.54,"q2":1.54,"q3":1.54,"max":1.54,"minLabel":"adapter_removal (TestData02)","maxLabel":"adapter_removal (TestData01)","q1Label":"adapter_removal (TestData02)","q2Label":"adapter_removal (TestData03)","q3Label":"adapter_removal (TestData03)"},"timeUsage":{"mean":0.7,"min":0.69,"q1":0.7,"q2":0.71,"q3":0.71,"max":0.71,"minLabel":"adapter_removal (TestData03)","maxLabel":"adapter_removal (TestData02)","q1Label":"adapter_removal (TestData03)","q2Label":"adapter_removal (TestData01)","q3Label":"adapter_removal (TestData01)"}},"preseq":{"cpu":null,"mem":null,"time":{"mean":67,"min":67,"q1":67,"q2":67,"q3":67,"max":67,"minLabel":"preseq (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","maxLabel":"preseq (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","q1Label":"preseq (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","q2Label":"preseq (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)","q3Label":"preseq (TestData02.pass_1.fastq.combined.fq.sorted.bam.filtered)"},"reads":null,"writes":null,"cpuUsage":null,"memUsage":null,"timeUsage":null},"samtools_idxstats":{"cpu":{"mean":101.6,"min":101.6,"q1":101.6,"q2":101.6,"q3":101.6,"max":101.6,"minLabel":"samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted)","maxLabel":"samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted)","q1Label":"samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted)","q2Label":"samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted)","q3Label":"samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted)"},"mem":{"mean":136445952,"min":136445952,"q1":136445952,"q2":136445952,"q3":136445952,"max":136445952,"minLabel":"samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted)","maxLabel":"samtools_idxstats (TestData02.pass_1.fastq.combined.fq.sorted)","q1Label":"samtools_idxstats 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Jun-07 16:43:01.268 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline Jun-07 16:43:01.479 [main] DEBUG nextflow.CacheDB - Closing CacheDB done Jun-07 16:43:01.498 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye