Jun-27 10:42:24.105 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/eager -r dev --pairedEnd --reads 'data/Sample1/Sample1.pass_{1,2}.fastq.gz' --fasta /home/keaton/Reference/EAGER/rCRS/rCRS.fasta --bwa_index /home/keaton/Reference/EAGER/rCRS/rCRS.fasta --fasta_index /home/keaton/Reference/EAGER/rCRS/rCRS.fasta.fai --outdir output/ --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 10 --max_memory 64.G --max_time 8.h -name DedupTest_Run1 Jun-27 10:42:24.227 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.01.0 Jun-27 10:42:25.467 [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-27 10:42:25.480 [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-27 10:42:25.578 [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-27 10:42:26.044 [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-27 10:42:26.044 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/eager` [DedupTest_Run1] - revision: ace20a08eb [dev] Jun-27 10:42:26.405 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/keaton/.nextflow/assets/nf-core/eager/nextflow.config Jun-27 10:42:26.443 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/keaton/.nextflow/assets/nf-core/eager/nextflow.config Jun-27 10:42:26.451 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` Jun-27 10:42:27.160 [main] DEBUG nextflow.Session - Session uuid: 38ee599d-f20c-40a1-a552-d43b071a4433 Jun-27 10:42:27.161 [main] DEBUG nextflow.Session - Run name: DedupTest_Run1 Jun-27 10:42:27.163 [main] DEBUG nextflow.Session - Executor pool size: 48 Jun-27 10:42:27.192 [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: 27825@info115 [10.10.10.115] CPUs: 48 - Mem: 252.4 GB (169.9 GB) - Swap: 1 GB (8 KB) Jun-27 10:42:27.246 [main] DEBUG nextflow.Session - Work-dir: /home/keaton/Projects/EAGER/DedupPOST/work [nfs] Jun-27 10:42:27.629 [main] DEBUG nextflow.Session - Session start invoked Jun-27 10:42:27.634 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start Jun-27 10:42:27.634 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/keaton/Projects/EAGER/DedupPOST/output/pipeline_info/execution_trace.txt Jun-27 10:42:27.637 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing Jun-27 10:42:28.444 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jun-27 10:42:28.574 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: data/Sample1/; pattern: Sample1.pass_{1,2}.fastq.gz; options: [:] Jun-27 10:42:28.588 [main] INFO nextflow.Nextflow - ---------------------------------------------------- ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/eager v2.0.7 ---------------------------------------------------- Jun-27 10:42:28.592 [main] INFO nextflow.Nextflow - Pipeline Name : nf-core/eager Pipeline Version : 2.0.7 Run Name : DedupTest_Run1 Reads : data/Sample1/Sample1.pass_{1,2}.fastq.gz Fasta Ref : /home/keaton/Reference/EAGER/rCRS/rCRS.fasta BAM Index Type : CSI BWA Index : /home/keaton/Reference/EAGER/rCRS/rCRS.fasta Data Type : Paired-End Skip Collapsing : No Skip Trimming : No Output stripped fastq: No Max Memory : 64.G Max CPUs : 10 Max Time : 8.h Output dir : output/ Working dir : /home/keaton/Projects/EAGER/DedupPOST/work Container Engine : null Current home : /home/keaton Current user : keaton Current path : /home/keaton/Projects/EAGER/DedupPOST Script dir : /home/keaton/.nextflow/assets/nf-core/eager Config Profile : standard Jun-27 10:42:28.592 [main] INFO nextflow.Nextflow - ---------------------------------------------------- Jun-27 10:42:28.662 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.662 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.668 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.670 [main] INFO nextflow.executor.Executor - [warm up] executor > local Jun-27 10:42:28.674 [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-27 10:42:28.678 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor Jun-27 10:42:28.678 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Jun-27 10:42:28.680 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local Jun-27 10:42:28.710 [main] DEBUG nextflow.Session - >>> barrier register (process: makeFastaIndex) Jun-27 10:42:28.712 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeFastaIndex -- maxForks: 48 Jun-27 10:42:28.737 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:makeSeqDict` matches process makeSeqDict Jun-27 10:42:28.740 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.740 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.740 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.741 [main] DEBUG nextflow.Session - >>> barrier register (process: makeSeqDict) Jun-27 10:42:28.742 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > makeSeqDict -- maxForks: 48 Jun-27 10:42:28.761 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:convertBam` matches process convertBam Jun-27 10:42:28.763 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.763 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.764 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.766 [main] DEBUG nextflow.Session - >>> barrier register (process: convertBam) Jun-27 10:42:28.766 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > convertBam -- maxForks: 48 Jun-27 10:42:28.782 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: convertBam) Jun-27 10:42:28.791 [Actor Thread 1] DEBUG nextflow.Session - <<< barrier arrive (process: makeFastaIndex) Jun-27 10:42:28.797 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:fastqc` matches process fastqc Jun-27 10:42:28.799 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.800 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.801 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.803 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc) Jun-27 10:42:28.803 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc -- maxForks: 48 Jun-27 10:42:28.813 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.814 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.814 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.815 [main] DEBUG nextflow.Session - >>> barrier register (process: fastp) Jun-27 10:42:28.815 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastp -- maxForks: 48 Jun-27 10:42:28.824 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: fastp) Jun-27 10:42:28.826 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.826 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.827 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.827 [main] DEBUG nextflow.Session - >>> barrier register (process: adapter_removal) Jun-27 10:42:28.827 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > adapter_removal -- maxForks: 48 Jun-27 10:42:28.841 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.842 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.842 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.843 [main] DEBUG nextflow.Session - >>> barrier register (process: fastqc_after_clipping) Jun-27 10:42:28.845 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > fastqc_after_clipping -- maxForks: 48 Jun-27 10:42:28.865 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:bwa` matches process bwa Jun-27 10:42:28.866 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.866 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.867 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.868 [main] DEBUG nextflow.Session - >>> barrier register (process: bwa) Jun-27 10:42:28.868 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bwa -- maxForks: 48 Jun-27 10:42:28.876 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.876 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.876 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.877 [main] DEBUG nextflow.Session - >>> barrier register (process: circulargenerator) Jun-27 10:42:28.877 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > circulargenerator -- maxForks: 48 Jun-27 10:42:28.883 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: circulargenerator) Jun-27 10:42:28.886 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.886 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.887 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.888 [main] DEBUG nextflow.Session - >>> barrier register (process: circularmapper) Jun-27 10:42:28.888 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > circularmapper -- maxForks: 48 Jun-27 10:42:28.893 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:42:28.893 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: circularmapper) Jun-27 10:42:28.899 [Task submitter] INFO nextflow.Session - [66/51c3c9] Submitted process > fastqc (Sample1.pass) Jun-27 10:42:28.900 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:bwamem` matches process bwamem Jun-27 10:42:28.901 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.901 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.901 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.902 [main] DEBUG nextflow.Session - >>> barrier register (process: bwamem) Jun-27 10:42:28.902 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bwamem -- maxForks: 48 Jun-27 10:42:28.909 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.909 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.909 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.910 [main] DEBUG nextflow.Session - >>> barrier register (process: samtools_flagstat) Jun-27 10:42:28.910 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > samtools_flagstat -- maxForks: 48 Jun-27 10:42:28.915 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.916 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.916 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.916 [main] DEBUG nextflow.Session - >>> barrier register (process: samtools_filter) Jun-27 10:42:28.916 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > samtools_filter -- maxForks: 48 Jun-27 10:42:28.918 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:42:28.919 [Task submitter] INFO nextflow.Session - [b8/eb6732] Submitted process > makeSeqDict (rCRS.fasta) Jun-27 10:42:28.923 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:strip_input_fastq` matches process strip_input_fastq Jun-27 10:42:28.924 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.924 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.924 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.924 [main] DEBUG nextflow.Session - >>> barrier register (process: strip_input_fastq) Jun-27 10:42:28.925 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > strip_input_fastq -- maxForks: 48 Jun-27 10:42:28.928 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.928 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:28.928 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:28.928 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:42:28.929 [main] DEBUG nextflow.Session - >>> barrier register (process: samtools_flagstat_after_filter) Jun-27 10:42:28.929 [Task submitter] INFO nextflow.Session - [6c/7b7b49] Submitted process > adapter_removal (Sample1.pass) Jun-27 10:42:28.929 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > samtools_flagstat_after_filter -- maxForks: 48 Jun-27 10:42:28.935 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:28.935 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.021 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.024 [main] DEBUG nextflow.Session - >>> barrier register (process: dedup) Jun-27 10:42:29.024 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dedup -- maxForks: 48 Jun-27 10:42:29.032 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:preseq` matches process preseq Jun-27 10:42:29.033 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:29.033 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.033 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.034 [main] DEBUG nextflow.Session - >>> barrier register (process: preseq) Jun-27 10:42:29.034 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > preseq -- maxForks: 48 Jun-27 10:42:29.040 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:damageprofiler` matches process damageprofiler Jun-27 10:42:29.041 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:29.041 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.041 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.042 [main] DEBUG nextflow.Session - >>> barrier register (process: damageprofiler) Jun-27 10:42:29.042 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > damageprofiler -- maxForks: 48 Jun-27 10:42:29.046 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:qualimap` matches process qualimap Jun-27 10:42:29.047 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:29.047 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.047 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.047 [main] DEBUG nextflow.Session - >>> barrier register (process: qualimap) Jun-27 10:42:29.047 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > qualimap -- maxForks: 48 Jun-27 10:42:29.050 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:markDup` matches process markDup Jun-27 10:42:29.051 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:29.051 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.051 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.052 [main] DEBUG nextflow.Session - >>> barrier register (process: markDup) Jun-27 10:42:29.052 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > markDup -- maxForks: 48 Jun-27 10:42:29.060 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:29.060 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.061 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.061 [main] DEBUG nextflow.Session - >>> barrier register (process: pmdtools) Jun-27 10:42:29.061 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > pmdtools -- maxForks: 48 Jun-27 10:42:29.065 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:bam_trim` matches process bam_trim Jun-27 10:42:29.066 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:29.066 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.066 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.066 [main] DEBUG nextflow.Session - >>> barrier register (process: bam_trim) Jun-27 10:42:29.066 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bam_trim -- maxForks: 48 Jun-27 10:42:29.070 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:29.070 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.070 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.071 [main] DEBUG nextflow.Session - >>> barrier register (process: output_documentation) Jun-27 10:42:29.071 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > output_documentation -- maxForks: 48 Jun-27 10:42:29.073 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:get_software_versions` matches process get_software_versions Jun-27 10:42:29.073 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:29.073 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.073 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.074 [main] DEBUG nextflow.Session - >>> barrier register (process: get_software_versions) Jun-27 10:42:29.074 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > get_software_versions -- maxForks: 48 Jun-27 10:42:29.169 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:multiqc` matches process multiqc Jun-27 10:42:29.170 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null Jun-27 10:42:29.170 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local' Jun-27 10:42:29.170 [main] DEBUG nextflow.executor.Executor - Initializing executor: local Jun-27 10:42:29.171 [main] DEBUG nextflow.Session - >>> barrier register (process: multiqc) Jun-27 10:42:29.172 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > multiqc -- maxForks: 48 Jun-27 10:42:29.175 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Jun-27 10:42:29.175 [main] DEBUG nextflow.Session - Session await Jun-27 10:42:29.199 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:42:29.200 [Task submitter] INFO nextflow.Session - [32/da0c98] Submitted process > output_documentation Jun-27 10:42:34.831 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: makeSeqDict (rCRS.fasta); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/b8/eb67329dc0afdd5fd3000ebaa7cb36] Jun-27 10:42:34.855 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: makeSeqDict) Jun-27 10:42:34.956 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: output_documentation; status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/32/da0c986198487b1b57900e88809e45] Jun-27 10:42:34.958 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: output_documentation) Jun-27 10:43:36.230 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: fastqc (Sample1.pass); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/66/51c3c9156f956937b7bed721cc30f9] Jun-27 10:43:36.251 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc) Jun-27 10:45:14.749 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: adapter_removal (Sample1.pass); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/6c/7b7b49cb8c7b9f8a216e6ed541918a] Jun-27 10:45:14.773 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: adapter_removal) Jun-27 10:45:14.785 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: bwamem) Jun-27 10:45:14.796 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:45:14.797 [Task submitter] INFO nextflow.Session - [5d/1498f4] Submitted process > fastqc_after_clipping (Sample1.pass_1.fastq) Jun-27 10:45:14.983 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:45:14.984 [Task submitter] INFO nextflow.Session - [6d/3f1cf8] Submitted process > bwa (Sample1.pass_1.fastq) Jun-27 10:45:52.998 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: fastqc_after_clipping (Sample1.pass_1.fastq); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/5d/1498f4e69219e6e9260456f88fdbb4] Jun-27 10:45:53.009 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: fastqc_after_clipping) Jun-27 10:45:58.189 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: bwa (Sample1.pass_1.fastq); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/6d/3f1cf8d2e21329f1b8901f1497a8b1] Jun-27 10:45:58.205 [Actor Thread 23] DEBUG nextflow.Session - <<< barrier arrive (process: strip_input_fastq) Jun-27 10:45:58.206 [Actor Thread 23] DEBUG nextflow.Session - <<< barrier arrive (process: bwa) Jun-27 10:45:58.219 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:45:58.220 [Task submitter] INFO nextflow.Session - [ae/eaeb90] Submitted process > samtools_flagstat (Sample1.pass_1.fastq.combined.fq.sorted) Jun-27 10:45:58.374 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:45:58.375 [Task submitter] INFO nextflow.Session - [81/e47fdc] Submitted process > samtools_filter (Sample1.pass_1.fastq.combined.fq.sorted.bam) Jun-27 10:45:59.716 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:45:59.717 [Task submitter] INFO nextflow.Session - [ba/30fb7a] Submitted process > damageprofiler (Sample1.pass_1.fastq.combined.fq.sorted) Jun-27 10:46:05.382 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: samtools_flagstat (Sample1.pass_1.fastq.combined.fq.sorted); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/ae/eaeb902b8598443a5a706e022cfe09] Jun-27 10:46:05.387 [Actor Thread 23] DEBUG nextflow.Session - <<< barrier arrive (process: samtools_flagstat) Jun-27 10:46:05.528 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: samtools_filter (Sample1.pass_1.fastq.combined.fq.sorted.bam); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/81/e47fdc61755ec76d037966145e8efa] Jun-27 10:46:05.603 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process samtools_filter > Skipping output binding because one or more optional files are missing: fileoutparam<1> Jun-27 10:46:05.603 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process samtools_filter > Skipping output binding because one or more optional files are missing: fileoutparam<2> Jun-27 10:46:05.606 [Actor Thread 8] DEBUG nextflow.Session - <<< barrier arrive (process: samtools_filter) Jun-27 10:46:05.609 [Actor Thread 23] DEBUG nextflow.Session - <<< barrier arrive (process: markDup) Jun-27 10:46:05.616 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:46:05.617 [Task submitter] INFO nextflow.Session - [b6/2db263] Submitted process > samtools_flagstat_after_filter (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered) Jun-27 10:46:05.697 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:46:05.697 [Task submitter] INFO nextflow.Session - [05/d73882] Submitted process > dedup (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered) Jun-27 10:46:05.703 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:46:05.703 [Task submitter] INFO nextflow.Session - [60/4d1512] Submitted process > qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered) Jun-27 10:46:05.974 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: samtools_flagstat_after_filter (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/b6/2db263d5045632df2585ef20f9a986] Jun-27 10:46:05.977 [Actor Thread 34] DEBUG nextflow.Session - <<< barrier arrive (process: samtools_flagstat_after_filter) Jun-27 10:46:15.924 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: damageprofiler (Sample1.pass_1.fastq.combined.fq.sorted); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/ba/30fb7aa5966a79a6883d66acfdc60e] Jun-27 10:46:15.935 [Actor Thread 34] DEBUG nextflow.Session - <<< barrier arrive (process: damageprofiler) Jun-27 10:46:15.992 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:46:15.993 [Task submitter] INFO nextflow.Session - [f2/406d86] Submitted process > get_software_versions (1) Jun-27 10:46:16.913 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/60/4d1512d99c9e6d0a8678286dc7a99f] Jun-27 10:46:16.920 [Actor Thread 34] DEBUG nextflow.Session - <<< barrier arrive (process: qualimap) Jun-27 10:46:22.001 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: dedup (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/05/d73882a95d281eb7365937e61de9c1] Jun-27 10:46:22.017 [Actor Thread 23] DEBUG nextflow.Session - <<< barrier arrive (process: dedup) Jun-27 10:46:22.019 [Actor Thread 23] DEBUG nextflow.Session - <<< barrier arrive (process: pmdtools) Jun-27 10:46:22.019 [Actor Thread 38] DEBUG nextflow.Session - <<< barrier arrive (process: bam_trim) Jun-27 10:46:22.053 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:46:22.054 [Task submitter] INFO nextflow.Session - [10/6c03a6] Submitted process > preseq (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered) Jun-27 10:46:28.180 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: preseq (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/10/6c03a69bf6b697bc403ba6249865d7] Jun-27 10:46:28.184 [Actor Thread 34] DEBUG nextflow.Session - <<< barrier arrive (process: preseq) Jun-27 10:46:32.662 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: get_software_versions (1); status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/f2/406d86b2b4ba03098ba1e11bb4a0d9] Jun-27 10:46:32.664 [Actor Thread 34] DEBUG nextflow.Session - <<< barrier arrive (process: get_software_versions) Jun-27 10:46:32.828 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-27 10:46:32.829 [Task submitter] INFO nextflow.Session - [39/915a81] Submitted process > multiqc Jun-27 10:46:44.336 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: multiqc; status: COMPLETED; exit: 0; error: -; workDir: /home/keaton/Projects/EAGER/DedupPOST/work/39/915a8103bd5000cc1841d6c64ecacc] Jun-27 10:46:44.355 [Actor Thread 34] DEBUG nextflow.Session - <<< barrier arrive (process: multiqc) Jun-27 10:46:44.356 [main] DEBUG nextflow.Session - Session await > all process finished Jun-27 10:46:44.359 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) Jun-27 10:46:44.359 [main] DEBUG nextflow.Session - Session await > all barriers passed Jun-27 10:46:45.183 [main] INFO nextflow.Nextflow - Warning, pipeline completed, but with errored process(es)  Jun-27 10:46:45.184 [main] INFO nextflow.Nextflow - Number of ignored errored process(es) : 0  Jun-27 10:46:45.184 [main] INFO nextflow.Nextflow - Number of successfully ran process(es) : 15  Jun-27 10:46:45.184 [main] INFO nextflow.Nextflow - [nf-core/eager] Pipeline completed successfully Jun-27 10:46:45.189 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=15; failedCount=0; ignoredCount=0; cachedCount=0; succeedDuration=11m 34s; failedDuration=0ms; cachedDuration=0ms] Jun-27 10:46:45.189 [main] DEBUG nextflow.trace.TraceFileObserver - Flow completing -- flushing trace file Jun-27 10:46:45.197 [main] DEBUG nextflow.trace.ReportObserver - Flow completing -- rendering html report Jun-27 10:46:45.298 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: 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(Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","maxLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q1Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q2Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q3Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)"},"mem":{"mean":7487774720,"min":7487774720,"q1":7487774720,"q2":7487774720,"q3":7487774720,"max":7487774720,"minLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","maxLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q1Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q2Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q3Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)"},"time":{"mean":6744,"min":6744,"q1":6744,"q2":6744,"q3":6744,"max":6744,"minLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","maxLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q1Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q2Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q3Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)"},"reads":null,"writes":{"mean":524288,"min":524288,"q1":524288,"q2":524288,"q3":524288,"max":524288,"minLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","maxLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q1Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q2Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q3Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)"},"cpuUsage":{"mean":111.48,"min":111.48,"q1":111.48,"q2":111.48,"q3":111.48,"max":111.48,"minLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","maxLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q1Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q2Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q3Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)"},"memUsage":{"mean":87.17,"min":87.17,"q1":87.17,"q2":87.17,"q3":87.17,"max":87.17,"minLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","maxLabel":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q1Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q2Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)","q3Label":"qualimap (Sample1.pass_1.fastq.combined.fq.sorted.bam.filtered)"},"timeUsage":{"mean":0.09,"min":0.09,"q1":0.09,"q2":0.09,"q3":0.09,"max":0.09,"minLabel":"qualimap 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(Sample1.pass)"},"time":{"mean":163572,"min":163572,"q1":163572,"q2":163572,"q3":163572,"max":163572,"minLabel":"adapter_removal (Sample1.pass)","maxLabel":"adapter_removal (Sample1.pass)","q1Label":"adapter_removal (Sample1.pass)","q2Label":"adapter_removal (Sample1.pass)","q3Label":"adapter_removal (Sample1.pass)"},"reads":{"mean":155189248,"min":155189248,"q1":155189248,"q2":155189248,"q3":155189248,"max":155189248,"minLabel":"adapter_removal (Sample1.pass)","maxLabel":"adapter_removal (Sample1.pass)","q1Label":"adapter_removal (Sample1.pass)","q2Label":"adapter_removal (Sample1.pass)","q3Label":"adapter_removal (Sample1.pass)"},"writes":{"mean":286433280,"min":286433280,"q1":286433280,"q2":286433280,"q3":286433280,"max":286433280,"minLabel":"adapter_removal (Sample1.pass)","maxLabel":"adapter_removal (Sample1.pass)","q1Label":"adapter_removal (Sample1.pass)","q2Label":"adapter_removal (Sample1.pass)","q3Label":"adapter_removal (Sample1.pass)"},"cpuUsage":{"mean":108.3,"min":108.3,"q1":108.3,"q2":108.3,"q3":108.3,"max":108.3,"minLabel":"adapter_removal (Sample1.pass)","maxLabel":"adapter_removal (Sample1.pass)","q1Label":"adapter_removal (Sample1.pass)","q2Label":"adapter_removal (Sample1.pass)","q3Label":"adapter_removal (Sample1.pass)"},"memUsage":{"mean":1.53,"min":1.53,"q1":1.53,"q2":1.53,"q3":1.53,"max":1.53,"minLabel":"adapter_removal (Sample1.pass)","maxLabel":"adapter_removal (Sample1.pass)","q1Label":"adapter_removal (Sample1.pass)","q2Label":"adapter_removal (Sample1.pass)","q3Label":"adapter_removal (Sample1.pass)"},"timeUsage":{"mean":2.27,"min":2.27,"q1":2.27,"q2":2.27,"q3":2.27,"max":2.27,"minLabel":"adapter_removal (Sample1.pass)","maxLabel":"adapter_removal (Sample1.pass)","q1Label":"adapter_removal (Sample1.pass)","q2Label":"adapter_removal (Sample1.pass)","q3Label":"adapter_removal 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Jun-27 10:46:46.332 [main] DEBUG nextflow.trace.TimelineObserver - Flow completing -- rendering html timeline Jun-27 10:46:46.563 [main] DEBUG nextflow.CacheDB - Closing CacheDB done Jun-27 10:46:46.615 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye