Jul-21 10:38:57.720 [main] DEBUG nextflow.cli.Launcher - $> nextflow -log /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/my.log run /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow -profile singularity -params-file /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/params.yaml -resume -c /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/custom_bind.config Jul-21 10:38:58.064 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.2 Jul-21 10:38:58.128 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/wynton/protected/home/rajkovic/jiqu/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.3 Jul-21 10:38:58.160 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jul-21 10:38:58.163 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jul-21 10:38:58.169 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Jul-21 10:38:58.208 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jul-21 10:39:01.033 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/nextflow.config Jul-21 10:39:01.039 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/custom_bind.config Jul-21 10:39:01.040 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/nextflow.config Jul-21 10:39:01.042 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/custom_bind.config Jul-21 10:39:01.140 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Jul-21 10:39:02.650 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Jul-21 10:39:02.685 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, uge, rosalind_uge, lugh, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, tigem, tubingen_apg, google, ipop_up, googlels, eddie, medair, bi, bigpurple, sbc_sharc, adcra, cedars, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, rosalind, hasta, cfc, uzh, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, mamba, wehi, awsbatch, imperial, maestro, genotoul, abims, janelia, nihbiowulf, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, sage, cambridge, podman, cheaha, xanadu, test, computerome, seg_globe, sanger, dkfz, pasteur, test_full, azurebatch, hki, crukmi, docker, engaging, gis, hypatia, psmn, eva, fgcz, conda, crg, singularity, prince, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawulf, uct_hpc, aws_tower, binac] Jul-21 10:39:02.700 [main] WARN nextflow.config.ConfigBuilder - It appears you have never run this project before -- Option `-resume` is ignored Jul-21 10:39:02.774 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Jul-21 10:39:02.847 [main] INFO nextflow.cli.CmdRun - Launching `/wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/main.nf` [desperate_leakey] DSL2 - revision: 7341307235 Jul-21 10:39:02.850 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jul-21 10:39:02.851 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] Jul-21 10:39:02.901 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /wynton/protected/home/rajkovic/jiqu/.nextflow/secrets/store.json Jul-21 10:39:02.911 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@14de1901] - activable => nextflow.secret.LocalSecretsProvider@14de1901 Jul-21 10:39:03.101 [main] DEBUG nextflow.Session - Session UUID: ca4d0a33-b3d4-4e6e-bb06-d40531d8e871 Jul-21 10:39:03.102 [main] DEBUG nextflow.Session - Run name: desperate_leakey Jul-21 10:39:03.103 [main] DEBUG nextflow.Session - Executor pool size: 256 Jul-21 10:39:03.138 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=768; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jul-21 10:39:03.510 [main] DEBUG nextflow.cli.CmdRun - Version: 23.04.2 build 5870 Created: 08-06-2023 08:29 UTC (01:29 PDT) System: Linux 3.10.0-1160.90.1.el7.x86_64 Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src Encoding: UTF-8 (UTF-8) Process: 114519@qb3-as15 [172.26.37.24] CPUs: 256 - Mem: 1007.8 GB (398.7 GB) - Swap: 4 GB (3.9 GB) Jul-21 10:39:03.612 [main] DEBUG nextflow.Session - Work-dir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work [fhgfs] Jul-21 10:39:03.678 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Jul-21 10:39:03.693 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Jul-21 10:39:03.798 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Jul-21 10:39:03.847 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 257; maxThreads: 1000 Jul-21 10:39:04.135 [main] DEBUG nextflow.Session - Session start Jul-21 10:39:04.564 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/output/pipeline_info/execution_trace_2023-07-21_10-39-02.txt Jul-21 10:39:04.652 [main] DEBUG nextflow.Session - Using default localLib path: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/lib Jul-21 10:39:04.663 [main] DEBUG nextflow.Session - Adding to the classpath library: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/lib Jul-21 10:39:04.665 [main] DEBUG nextflow.Session - Adding to the classpath library: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/lib/nfcore_external_java_deps.jar Jul-21 10:39:06.528 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jul-21 10:39:06.874 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/chipseq v2.0.0 ------------------------------------------------------ Core Nextflow options runName : desperate_leakey containerEngine : singularity launchDir : /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA workDir : /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work projectDir : /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow userName : jiqu profile : singularity configFiles : /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/nextflow.config, /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/custom_bind.config Input/output options input : /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test_data/samplesheet.csv read_length : 50 outdir : /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/output email : jiahua.qu@ucsf.edu Reference genome options fasta : /wynton/group/rajkovic/jiahua/software/NextFlow/genome/NCBI/GRCm38/references/Mus_musculus/NCBI/GRCm38/Sequence/WholeGenomeFasta/genome.fa gtf : /wynton/group/rajkovic/jiahua/software/NextFlow/genome/NCBI/GRCm38/references/Mus_musculus/NCBI/GRCm38/Annotation/Genes/genes.gtf bwa_index : /wynton/group/rajkovic/jiahua/software/NextFlow/genome/NCBI/GRCm38/references/Mus_musculus/NCBI/GRCm38/Sequence/BWAIndex gene_bed : /wynton/group/rajkovic/jiahua/software/NextFlow/genome/NCBI/GRCm38/references/Mus_musculus/NCBI/GRCm38/Annotation/Genes/genes.bed macs_gsize : 2307679482 blacklist : /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/assets/blacklists/v2.0/GRCm38-blacklist.v2.bed save_reference : true Adapter trimming options save_trimmed : true Peak calling options narrow_peak : true macs_fdr : 0.05 save_macs_pileup : true Institutional config options custom_config_base: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/../configs/ !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/chipseq for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.3240506 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/chipseq/blob/master/CITATIONS.md ------------------------------------------------------ Jul-21 10:40:04.777 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Jul-21 10:40:04.781 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_GETCHROMSIZES` matches process NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Jul-21 10:40:04.791 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:04.792 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:04.817 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Jul-21 10:40:04.830 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=256; memory=1007.8 GB; capacity=256; pollInterval=100ms; dumpInterval=5m Jul-21 10:40:05.057 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GENOME_BLACKLIST_REGIONS` matches process NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:GENOME_BLACKLIST_REGIONS Jul-21 10:40:05.062 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.063 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.083 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK` matches process NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK Jul-21 10:40:05.086 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.086 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.370 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC Jul-21 10:40:05.372 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQC_TRIMGALORE:FASTQC` matches process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC Jul-21 10:40:05.377 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.378 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.398 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE Jul-21 10:40:05.602 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQC_TRIMGALORE:TRIMGALORE` matches process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE Jul-21 10:40:05.607 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.608 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.629 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM Jul-21 10:40:05.630 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BWA_MEM` matches process NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM Jul-21 10:40:05.632 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.634 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.645 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT Jul-21 10:40:05.648 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT` matches process NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT Jul-21 10:40:05.650 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.650 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.663 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX Jul-21 10:40:05.665 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX` matches process NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX Jul-21 10:40:05.667 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.668 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.685 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jul-21 10:40:05.687 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_.*` matches process NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jul-21 10:40:05.690 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.691 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.699 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jul-21 10:40:05.700 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_.*` matches process NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jul-21 10:40:05.701 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.702 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.708 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jul-21 10:40:05.709 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_.*` matches process NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jul-21 10:40:05.711 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.711 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.743 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:PICARD_MERGESAMFILES Jul-21 10:40:05.745 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PICARD_MERGESAMFILES` matches process NFCORE_CHIPSEQ:CHIPSEQ:PICARD_MERGESAMFILES Jul-21 10:40:05.747 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.748 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.757 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES Jul-21 10:40:05.759 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES` matches process NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES Jul-21 10:40:05.760 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.761 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.769 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX Jul-21 10:40:05.770 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX` matches process NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX Jul-21 10:40:05.772 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.773 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.781 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jul-21 10:40:05.783 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jul-21 10:40:05.785 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.786 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.796 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jul-21 10:40:05.798 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jul-21 10:40:05.801 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.802 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.812 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jul-21 10:40:05.813 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jul-21 10:40:05.814 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.815 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.826 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER Jul-21 10:40:05.827 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BAM_FILTER` matches process NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER Jul-21 10:40:05.830 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.831 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.837 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_REMOVE_ORPHANS Jul-21 10:40:05.839 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BAM_REMOVE_ORPHANS` matches process NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_REMOVE_ORPHANS Jul-21 10:40:05.842 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.843 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.850 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT Jul-21 10:40:05.851 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT` matches process NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT Jul-21 10:40:05.852 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.853 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.859 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX Jul-21 10:40:05.859 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX` matches process NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX Jul-21 10:40:05.860 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.861 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.874 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jul-21 10:40:05.876 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jul-21 10:40:05.877 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.878 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.886 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jul-21 10:40:05.888 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jul-21 10:40:05.890 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.890 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.897 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jul-21 10:40:05.898 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jul-21 10:40:05.900 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.900 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.918 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium,error_ignore` for process with name NFCORE_CHIPSEQ:CHIPSEQ:PRESEQ_LCEXTRAP Jul-21 10:40:05.919 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:error_ignore` matches labels `process_medium,error_ignore` for process with name NFCORE_CHIPSEQ:CHIPSEQ:PRESEQ_LCEXTRAP Jul-21 10:40:05.920 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PRESEQ_LCEXTRAP` matches process NFCORE_CHIPSEQ:CHIPSEQ:PRESEQ_LCEXTRAP Jul-21 10:40:05.922 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.923 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.933 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:PICARD_COLLECTMULTIPLEMETRICS Jul-21 10:40:05.934 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PICARD_COLLECTMULTIPLEMETRICS` matches process NFCORE_CHIPSEQ:CHIPSEQ:PICARD_COLLECTMULTIPLEMETRICS Jul-21 10:40:05.936 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.937 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.945 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS Jul-21 10:40:05.946 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PHANTOMPEAKQUALTOOLS` matches process NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS Jul-21 10:40:05.948 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.949 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.960 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS` matches process NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS Jul-21 10:40:05.962 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.963 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.973 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:BEDTOOLS_GENOMECOV Jul-21 10:40:05.974 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV` matches process NFCORE_CHIPSEQ:CHIPSEQ:BEDTOOLS_GENOMECOV Jul-21 10:40:05.977 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.977 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.988 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:UCSC_BEDGRAPHTOBIGWIG Jul-21 10:40:05.990 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_CHIPSEQ:CHIPSEQ:UCSC_BEDGRAPHTOBIGWIG Jul-21 10:40:05.992 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:05.993 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:05.999 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_COMPUTEMATRIX Jul-21 10:40:06.000 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DEEPTOOLS_COMPUTEMATRIX` matches process NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_COMPUTEMATRIX Jul-21 10:40:06.002 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.003 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.012 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTPROFILE Jul-21 10:40:06.014 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DEEPTOOLS_PLOTPROFILE` matches process NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTPROFILE Jul-21 10:40:06.015 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.016 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.023 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTHEATMAP Jul-21 10:40:06.024 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DEEPTOOLS_PLOTHEATMAP` matches process NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTHEATMAP Jul-21 10:40:06.025 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.026 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.069 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTFINGERPRINT Jul-21 10:40:06.070 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DEEPTOOLS_PLOTFINGERPRINT` matches process NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTFINGERPRINT Jul-21 10:40:06.071 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.072 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.084 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CALLPEAK Jul-21 10:40:06.085 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MACS2_CALLPEAK` matches process NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CALLPEAK Jul-21 10:40:06.087 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.088 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.107 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:FRIP_SCORE Jul-21 10:40:06.108 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FRIP_SCORE` matches process NFCORE_CHIPSEQ:CHIPSEQ:FRIP_SCORE Jul-21 10:40:06.111 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.111 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.126 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC_CUSTOM_PEAKS` matches process NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC_CUSTOM_PEAKS Jul-21 10:40:06.128 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.129 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.134 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:HOMER_ANNOTATEPEAKS_MACS2 Jul-21 10:40:06.135 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:HOMER_ANNOTATEPEAKS_MACS2` matches process NFCORE_CHIPSEQ:CHIPSEQ:HOMER_ANNOTATEPEAKS_MACS2 Jul-21 10:40:06.137 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.138 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.165 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:PLOT_MACS2_QC Jul-21 10:40:06.166 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLOT_MACS2_QC` matches process NFCORE_CHIPSEQ:CHIPSEQ:PLOT_MACS2_QC Jul-21 10:40:06.167 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.173 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.183 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:PLOT_HOMER_ANNOTATEPEAKS Jul-21 10:40:06.184 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:PLOT_HOMER_ANNOTATEPEAKS` matches process NFCORE_CHIPSEQ:CHIPSEQ:PLOT_HOMER_ANNOTATEPEAKS Jul-21 10:40:06.187 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.188 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.200 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_long` for process with name NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS Jul-21 10:40:06.201 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MACS2_CONSENSUS` matches process NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS Jul-21 10:40:06.204 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.205 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.214 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:HOMER_ANNOTATEPEAKS_CONSENSUS Jul-21 10:40:06.215 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:HOMER_ANNOTATEPEAKS_CONSENSUS` matches process NFCORE_CHIPSEQ:CHIPSEQ:HOMER_ANNOTATEPEAKS_CONSENSUS Jul-21 10:40:06.217 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.217 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.226 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:ANNOTATE_BOOLEAN_PEAKS Jul-21 10:40:06.228 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ANNOTATE_BOOLEAN_PEAKS` matches process NFCORE_CHIPSEQ:CHIPSEQ:ANNOTATE_BOOLEAN_PEAKS Jul-21 10:40:06.230 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.231 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.246 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:SUBREAD_FEATURECOUNTS Jul-21 10:40:06.249 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SUBREAD_FEATURECOUNTS` matches process NFCORE_CHIPSEQ:CHIPSEQ:SUBREAD_FEATURECOUNTS Jul-21 10:40:06.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.251 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.266 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:DESEQ2_QC Jul-21 10:40:06.267 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:DESEQ2_QC` matches process NFCORE_CHIPSEQ:CHIPSEQ:DESEQ2_QC Jul-21 10:40:06.269 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.270 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.313 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:IGV` matches process NFCORE_CHIPSEQ:CHIPSEQ:IGV Jul-21 10:40:06.315 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.317 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.414 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_CHIPSEQ:CHIPSEQ:CUSTOM_DUMPSOFTWAREVERSIONS Jul-21 10:40:06.415 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_CHIPSEQ:CHIPSEQ:CUSTOM_DUMPSOFTWAREVERSIONS Jul-21 10:40:06.417 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.417 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.467 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC Jul-21 10:40:06.469 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC Jul-21 10:40:06.472 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jul-21 10:40:06.472 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jul-21 10:40:06.498 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: NFCORE_CHIPSEQ:CHIPSEQ:UCSC_BEDGRAPHTOBIGWIG, NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CALLPEAK, NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS, PLOT_MACS2_QC, NFCORE_CHIPSEQ:CHIPSEQ:PICARD_MERGESAMFILES, NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, BWA_MEM, GFFREAD, NFCORE_CHIPSEQ:CHIPSEQ:SUBREAD_FEATURECOUNTS, BAM_REMOVE_ORPHANS, GUNZIP, SAMTOOLS_STATS, GUNZIP_GFF, NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC_CUSTOM_PEAKS, PICARD_MERGESAMFILES, TRIMGALORE, BEDTOOLS_GENOMECOV, NFCORE_CHIPSEQ:CHIPSEQ:PRESEQ_LCEXTRAP, NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, CHROMAP_CHROMAP, NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, BOWTIE2_ALIGN, MACS2_CONSENSUS, SAMTOOLS_INDEX, HOMER_ANNOTATEPEAKS_MACS2, PRESEQ_LCEXTRAP, NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS, FASTQC, NFCORE_CHIPSEQ:CHIPSEQ:HOMER_ANNOTATEPEAKS_MACS2, NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS, NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTPROFILE, DEEPTOOLS_PLOTFINGERPRINT, UCSC_BEDGRAPHTOBIGWIG, MULTIQC, GTF2BED, PHANTOMPEAKQUALTOOLS, GUNZIP_GTF, UNTAR_BOWTIE2_INDEX, NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX, NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_REMOVE_ORPHANS, NFCORE_CHIPSEQ:CHIPSEQ:PLOT_MACS2_QC, GENOME_BLACKLIST_REGIONS, NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT, SAMTOOLS_FLAGSTAT, SAMPLESHEET_CHECK, NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT, GUNZIP_FASTA, DEEPTOOLS_COMPUTEMATRIX, MACS2_CALLPEAK, HOMER_ANNOTATEPEAKS_CONSENSUS, NFCORE_CHIPSEQ:CHIPSEQ:PLOT_HOMER_ANNOTATEPEAKS, NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC, NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, DEEPTOOLS_PLOTPROFILE, HOMER_ANNOTATEPEAKS, NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES, NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC, ANNOTATE_BOOLEAN_PEAKS, KHMER_UNIQUEKMERS, NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER, DESEQ2_QC, PICARD_MARKDUPLICATES, NFCORE_CHIPSEQ:CHIPSEQ:FRIP_SCORE, UNTAR_CHROMAP_INDEX, UNTAR, DEEPTOOLS_PLOTHEATMAP, NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK, NFCORE_CHIPSEQ:CHIPSEQ:BEDTOOLS_GENOMECOV, NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTHEATMAP, NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_COMPUTEMATRIX, NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES, NFCORE_CHIPSEQ:CHIPSEQ:DESEQ2_QC, STAR_ALIGN, NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM, NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE, GUNZIP_BLACKLIST, PICARD_COLLECTMULTIPLEMETRICS, BOWTIE2_BUILD, CUSTOM_GETCHROMSIZES, SAMTOOLS_SORT, FRIP_SCORE, NFCORE_CHIPSEQ:CHIPSEQ:HOMER_ANNOTATEPEAKS_CONSENSUS, SUBREAD_FEATURECOUNTS, NFCORE_CHIPSEQ:CHIPSEQ:ANNOTATE_BOOLEAN_PEAKS, MULTIQC_CUSTOM_PEAKS, GUNZIP_GENE_BED, UNTAR_STAR_INDEX, NFCORE_CHIPSEQ:CHIPSEQ:PICARD_COLLECTMULTIPLEMETRICS, BWA_INDEX, NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:GENOME_BLACKLIST_REGIONS, NFCORE_CHIPSEQ:CHIPSEQ:IGV, NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX, UNTAR_BWA_INDEX, NFCORE_CHIPSEQ:CHIPSEQ:CUSTOM_DUMPSOFTWAREVERSIONS, PLOT_HOMER_ANNOTATEPEAKS, NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX, CHROMAP_INDEX, NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTFINGERPRINT, SAMTOOLS_IDXSTATS, IGV, CUSTOM_DUMPSOFTWAREVERSIONS, STAR_GENOMEGENERATE, MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS, NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, BAM_FILTER Jul-21 10:40:06.513 [main] DEBUG nextflow.Session - Igniting dataflow network (92) Jul-21 10:40:06.526 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Jul-21 10:40:06.528 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:GENOME_BLACKLIST_REGIONS Jul-21 10:40:06.532 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK Jul-21 10:40:06.534 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC Jul-21 10:40:06.535 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE Jul-21 10:40:06.537 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM Jul-21 10:40:06.538 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT Jul-21 10:40:06.540 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX Jul-21 10:40:06.542 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jul-21 10:40:06.544 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jul-21 10:40:06.545 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jul-21 10:40:06.545 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:PICARD_MERGESAMFILES Jul-21 10:40:06.546 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES Jul-21 10:40:06.547 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX Jul-21 10:40:06.548 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jul-21 10:40:06.549 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jul-21 10:40:06.549 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jul-21 10:40:06.550 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_FILTER Jul-21 10:40:06.551 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_REMOVE_ORPHANS Jul-21 10:40:06.551 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT Jul-21 10:40:06.552 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX Jul-21 10:40:06.552 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jul-21 10:40:06.553 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jul-21 10:40:06.553 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jul-21 10:40:06.554 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:PRESEQ_LCEXTRAP Jul-21 10:40:06.555 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:PICARD_COLLECTMULTIPLEMETRICS Jul-21 10:40:06.556 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS Jul-21 10:40:06.557 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS Jul-21 10:40:06.558 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:BEDTOOLS_GENOMECOV Jul-21 10:40:06.558 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:UCSC_BEDGRAPHTOBIGWIG Jul-21 10:40:06.559 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_COMPUTEMATRIX Jul-21 10:40:06.561 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTPROFILE Jul-21 10:40:06.561 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTHEATMAP Jul-21 10:40:06.562 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:DEEPTOOLS_PLOTFINGERPRINT Jul-21 10:40:06.564 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CALLPEAK Jul-21 10:40:06.564 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:FRIP_SCORE Jul-21 10:40:06.565 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC_CUSTOM_PEAKS Jul-21 10:40:06.566 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:HOMER_ANNOTATEPEAKS_MACS2 Jul-21 10:40:06.568 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:PLOT_MACS2_QC Jul-21 10:40:06.568 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:PLOT_HOMER_ANNOTATEPEAKS Jul-21 10:40:06.569 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS Jul-21 10:40:06.570 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:HOMER_ANNOTATEPEAKS_CONSENSUS Jul-21 10:40:06.571 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:ANNOTATE_BOOLEAN_PEAKS Jul-21 10:40:06.571 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:SUBREAD_FEATURECOUNTS Jul-21 10:40:06.572 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:DESEQ2_QC Jul-21 10:40:06.573 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:IGV Jul-21 10:40:06.573 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:CUSTOM_DUMPSOFTWAREVERSIONS Jul-21 10:40:06.574 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC Jul-21 10:40:06.574 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Jul-21 10:40:06.575 [main] DEBUG nextflow.Session - Session await Jul-21 10:40:06.695 [Actor Thread 256] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/python:3.8.3; path=/wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/../singularity-images/depot.galaxyproject.org-singularity-python-3.8.3.img Jul-21 10:40:06.695 [Actor Thread 251] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0; path=/wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/../singularity-images/depot.galaxyproject.org-singularity-samtools-1.15.1--h1170115_0.img Jul-21 10:40:06.736 [Actor Thread 255] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.003 s; external sort time: 0.019 s; total time: 0.022 s Jul-21 10:40:06.959 [Actor Thread 255] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/collect-file/ed89d6a11c4aa2ea0852ece92f5c02cb Jul-21 10:40:06.975 [Actor Thread 255] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/371946.1.long.q/nxf-4361702441886530209 Jul-21 10:40:07.089 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:07.112 [Task submitter] INFO nextflow.Session - [cb/aabcfa] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) Jul-21 10:40:07.138 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:07.140 [Task submitter] INFO nextflow.Session - [ce/e4e4a6] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa) Jul-21 10:40:09.905 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/cb/aabcfa57424a21803da847dde7adfa] Jul-21 10:40:09.974 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=768; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jul-21 10:40:10.023 [Actor Thread 239] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0; path=/wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/../singularity-images/depot.galaxyproject.org-singularity-trim-galore-0.6.7--hdfd78af_0.img Jul-21 10:40:10.023 [Actor Thread 237] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0; path=/wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/../singularity-images/depot.galaxyproject.org-singularity-fastqc-0.11.9--0.img Jul-21 10:40:10.061 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.063 [Task submitter] INFO nextflow.Session - [36/5e8fc5] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Smad2_IP_REP1_T1) Jul-21 10:40:10.125 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.126 [Task submitter] INFO nextflow.Session - [68/cb50a5] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Smad2_IP_REP2_T1) Jul-21 10:40:10.139 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.140 [Task submitter] INFO nextflow.Session - [ff/d97096] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Input_REP1_T1) Jul-21 10:40:10.150 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.151 [Task submitter] INFO nextflow.Session - [24/a234a9] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Input_REP2_T1) Jul-21 10:40:10.163 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.165 [Task submitter] INFO nextflow.Session - [51/4ea2be] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Input_REP2_T1) Jul-21 10:40:10.178 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.179 [Task submitter] INFO nextflow.Session - [94/333a16] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Smad2_IP_REP1_T1) Jul-21 10:40:10.191 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.192 [Task submitter] INFO nextflow.Session - [bf/4983ba] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Smad2_IP_REP2_T1) Jul-21 10:40:10.205 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.206 [Task submitter] INFO nextflow.Session - [77/de1c3f] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Input_REP1_T1) Jul-21 10:40:10.220 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.221 [Task submitter] INFO nextflow.Session - [9a/b9d3c6] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Input_REP1_T1) Jul-21 10:40:10.242 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.245 [Task submitter] INFO nextflow.Session - [99/9b0812] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Smad2_IP_REP1_T1) Jul-21 10:40:10.257 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.258 [Task submitter] INFO nextflow.Session - [43/4d8f8d] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Input_REP1_T1) Jul-21 10:40:10.273 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.275 [Task submitter] INFO nextflow.Session - [8b/cca7ca] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Input_REP2_T1) Jul-21 10:40:10.286 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.288 [Task submitter] INFO nextflow.Session - [45/2ddb9d] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Smad2_IP_REP1_T1) Jul-21 10:40:10.302 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.304 [Task submitter] INFO nextflow.Session - [3d/096b52] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Smad2_IP_REP2_T1) Jul-21 10:40:10.314 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.316 [Task submitter] INFO nextflow.Session - [be/a94060] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Input_REP2_T1) Jul-21 10:40:10.350 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:10.351 [Task submitter] INFO nextflow.Session - [b6/a92377] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Smad2_IP_REP2_T1) Jul-21 10:40:39.913 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/ce/e4e4a65fcdb787a5abed12898b04b5] Jul-21 10:40:39.943 [Actor Thread 256] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0; path=/wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/../singularity-images/depot.galaxyproject.org-singularity-bedtools-2.30.0--hc088bd4_0.img Jul-21 10:40:39.964 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:40:39.966 [Task submitter] INFO nextflow.Session - [92/8d4c18] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:GENOME_BLACKLIST_REGIONS (genome.fa.sizes) Jul-21 10:40:42.627 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: NFCORE_CHIPSEQ:CHIPSEQ:PREPARE_GENOME:GENOME_BLACKLIST_REGIONS (genome.fa.sizes); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/92/8d4c1833fef11f8c342775445d9fee] Jul-21 10:45:04.955 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 16 -- submitted tasks are shown below ~> TaskHandler[id: 8; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Smad2_IP_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/36/5e8fc523e53423e5c1dd61fc187758] ~> TaskHandler[id: 9; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Smad2_IP_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/68/cb50a58179d7abb22f559cb8750159] ~> TaskHandler[id: 11; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Input_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/ff/d97096502958ecc496638c36afebd6] ~> TaskHandler[id: 13; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Input_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/24/a234a9971dad5fdd653781bffc488c] ~> TaskHandler[id: 5; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Input_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/51/4ea2be9c117a3facfcc87063c50248] ~> TaskHandler[id: 16; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Smad2_IP_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/94/333a16ae29b1635cd4b85da64a5e71] ~> TaskHandler[id: 17; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Smad2_IP_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/bf/4983ba6b16373cb9135bc2ee965f1e] ~> TaskHandler[id: 3; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Input_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/77/de1c3ff02795e10ec6da08e94126bc] ~> TaskHandler[id: 4; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Input_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/9a/b9d3c6d9b8cacd6713f5d61be39d4e] ~> TaskHandler[id: 15; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Smad2_IP_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/99/9b081223b465b735dbe642156a4bc1] .. remaining tasks omitted. Jul-21 10:46:20.910 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Smad2_IP_REP1_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/94/333a16ae29b1635cd4b85da64a5e71] Jul-21 10:47:11.440 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Smad2_IP_REP2_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/bf/4983ba6b16373cb9135bc2ee965f1e] Jul-21 10:47:17.538 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Smad2_IP_REP1_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/99/9b081223b465b735dbe642156a4bc1] Jul-21 10:47:17.805 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jul-21 10:47:17.816 [Actor Thread 254] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0; path=/wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/nf-core-chipseq-2.0.0/workflow/../singularity-images/depot.galaxyproject.org-singularity-mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40-8110a70be2bfe7f75a2ea7f2a89cda4cc7732095-0.img Jul-21 10:47:17.844 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jul-21 10:47:17.846 [Task submitter] INFO nextflow.Session - [a2/47aba5] Submitted process > NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (ES_Smad2_IP_REP1_T1) Jul-21 10:47:21.981 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (ES_Smad2_IP_REP1_T1); status: COMPLETED; exit: 1; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/a2/47aba59b81052ee234b8e73e115091] Jul-21 10:47:21.991 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (ES_Smad2_IP_REP1_T1); work-dir=/wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/a2/47aba59b81052ee234b8e73e115091 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (ES_Smad2_IP_REP1_T1)` terminated with an error exit status (1) Jul-21 10:47:22.025 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (ES_Smad2_IP_REP1_T1)' Caused by: Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (ES_Smad2_IP_REP1_T1)` terminated with an error exit status (1) Command executed: INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'` bwa mem \ -M -R '@RG\tID:ES_Smad2_IP_REP1_T1\tSM:ES_Smad2_IP_REP1\tPL:ILLUMINA\tLB:ES_Smad2_IP_REP1_T1\tPU:1' \ -t 12 \ $INDEX \ ES_Smad2_IP_REP1_T1_trimmed.fq.gz \ | samtools view -bhS -F 0x0100 -O BAM --threads 12 -o ES_Smad2_IP_REP1_T1.Lb.bam - cat <<-END_VERSIONS > versions.yml "NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM": bwa: $(echo $(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*$//') samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//') END_VERSIONS Command exit status: 1 Command output: (empty) Command error: -y INT seed occurrence for the 3rd round seeding [20] -c INT skip seeds with more than INT occurrences [500] -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50] -W INT discard a chain if seeded bases shorter than INT [0] -m INT perform at most INT rounds of mate rescues for each read [50] -S skip mate rescue -P skip pairing; mate rescue performed unless -S also in use Scoring options: -A INT score for a sequence match, which scales options -TdBOELU unless overridden [1] -B INT penalty for a mismatch [4] -O INT[,INT] gap open penalties for deletions and insertions [6,6] -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1] -L INT[,INT] penalty for 5'- and 3'-end clipping [5,5] -U INT penalty for an unpaired read pair [17] -x STR read type. Setting -x changes multiple parameters unless overridden [null] pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 (PacBio reads to ref) ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 (Oxford Nanopore 2D-reads to ref) intractg: -B9 -O16 -L5 (intra-species contigs to ref) Input/output options: -p smart pairing (ignoring in2.fq) -R STR read group header line such as '@RG\tID:foo\tSM:bar' [null] -H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null] -o FILE sam file to output results to [stdout] -j treat ALT contigs as part of the primary assembly (i.e. ignore .alt file) -5 for split alignment, take the alignment with the smallest coordinate as primary -q don't modify mapQ of supplementary alignments -K INT process INT input bases in each batch regardless of nThreads (for reproducibility) [] -v INT verbosity level: 1=error, 2=warning, 3=message, 4+=debugging [3] -T INT minimum score to output [30] -h INT[,INT] if there are 80% of the max score, output all in XA [5,200] -a output all alignments for SE or unpaired PE -C append FASTA/FASTQ comment to SAM output -V output the reference FASTA header in the XR tag -Y use soft clipping for supplementary alignments -M mark shorter split hits as secondary -I FLOAT[,FLOAT[,INT[,INT]]] specify the mean, standard deviation (10% of the mean if absent), max (4 sigma from the mean if absent) and min of the insert size distribution. FR orientation only. [inferred] Note: Please read the man page for detailed description of the command line and options. [main_samview] fail to read the header from "-". Work dir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/a2/47aba59b81052ee234b8e73e115091 Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` Jul-21 10:47:22.039 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Jul-21 10:47:29.028 [main] DEBUG nextflow.Session - Session await > all processes finished Jul-21 10:47:29.057 [Actor Thread 243] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 5; slices: 1; internal sort time: 0.023 s; external sort time: 0.001 s; total time: 0.024 s Jul-21 10:47:29.076 [Actor Thread 243] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/collect-file/24a28d91a9023ce167a0f3fca285b192 Jul-21 10:47:29.079 [Actor Thread 243] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/371946.1.long.q/nxf-907671475061316649 Jul-21 10:47:47.113 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Smad2_IP_REP2_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/b6/a92377284041bc2f108139c1759ab0] Jul-21 10:47:47.170 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jul-21 10:50:05.009 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 12 -- submitted tasks are shown below ~> TaskHandler[id: 8; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Smad2_IP_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/36/5e8fc523e53423e5c1dd61fc187758] ~> TaskHandler[id: 9; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Smad2_IP_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/68/cb50a58179d7abb22f559cb8750159] ~> TaskHandler[id: 11; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Input_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/ff/d97096502958ecc496638c36afebd6] ~> TaskHandler[id: 13; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Input_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/24/a234a9971dad5fdd653781bffc488c] ~> TaskHandler[id: 5; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Input_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/51/4ea2be9c117a3facfcc87063c50248] ~> TaskHandler[id: 3; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Input_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/77/de1c3ff02795e10ec6da08e94126bc] ~> TaskHandler[id: 4; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Input_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/9a/b9d3c6d9b8cacd6713f5d61be39d4e] ~> TaskHandler[id: 12; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Input_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/43/4d8f8da333553b2db11efbec0947b1] ~> TaskHandler[id: 6; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Input_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/8b/cca7ca911401b5cee08d85e0977ffa] ~> TaskHandler[id: 7; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Smad2_IP_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/45/2ddb9dadf29ee76dc44437de90674a] .. remaining tasks omitted. Jul-21 10:51:12.560 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Smad2_IP_REP2_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/68/cb50a58179d7abb22f559cb8750159] Jul-21 10:51:16.555 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Smad2_IP_REP1_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/36/5e8fc523e53423e5c1dd61fc187758] Jul-21 10:52:19.596 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Smad2_IP_REP1_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/45/2ddb9dadf29ee76dc44437de90674a] Jul-21 10:52:19.634 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jul-21 10:53:12.325 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Smad2_IP_REP2_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/3d/096b52c63df59d33adf7f6a9968bad] Jul-21 10:53:12.363 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jul-21 10:53:36.834 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Input_REP1_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/77/de1c3ff02795e10ec6da08e94126bc] Jul-21 10:54:47.915 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Input_REP1_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/ff/d97096502958ecc496638c36afebd6] Jul-21 10:55:05.031 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below ~> TaskHandler[id: 13; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Input_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/24/a234a9971dad5fdd653781bffc488c] ~> TaskHandler[id: 5; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Input_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/51/4ea2be9c117a3facfcc87063c50248] ~> TaskHandler[id: 4; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Input_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/9a/b9d3c6d9b8cacd6713f5d61be39d4e] ~> TaskHandler[id: 12; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Input_REP1_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/43/4d8f8da333553b2db11efbec0947b1] ~> TaskHandler[id: 6; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Input_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/8b/cca7ca911401b5cee08d85e0977ffa] ~> TaskHandler[id: 14; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Input_REP2_T1); status: RUNNING; exit: -; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/be/a94060f9de06564db658ae689d1d5f] Jul-21 10:55:10.212 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (EBAC_Input_REP2_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/51/4ea2be9c117a3facfcc87063c50248] Jul-21 10:55:28.665 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Input_REP1_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/9a/b9d3c6d9b8cacd6713f5d61be39d4e] Jul-21 10:55:28.706 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jul-21 10:55:52.645 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:FASTQC (ES_Input_REP2_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/24/a234a9971dad5fdd653781bffc488c] Jul-21 10:56:58.641 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Input_REP2_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/be/a94060f9de06564db658ae689d1d5f] Jul-21 10:56:58.683 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jul-21 10:57:25.164 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (ES_Input_REP1_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/43/4d8f8da333553b2db11efbec0947b1] Jul-21 10:57:25.432 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jul-21 10:57:26.161 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE (EBAC_Input_REP2_T1); status: COMPLETED; exit: 0; error: -; workDir: /wynton/group/rajkovic/jiahua/test/09-test_NextFlow-nf-core-chipseq/test/BWA/work/8b/cca7ca911401b5cee08d85e0977ffa] Jul-21 10:57:26.222 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_CHIPSEQ:CHIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jul-21 10:57:26.234 [main] DEBUG nextflow.Session - Session await > all barriers passed Jul-21 10:57:31.249 [main] INFO nextflow.util.ThreadPoolHelper - Waiting for file transfers to complete (2 files) Jul-21 10:58:21.582 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Jul-21 10:58:21.836 [main] INFO nextflow.Nextflow - -[nf-core/chipseq] Sent summary e-mail to jiahua.qu@ucsf.edu (sendmail)- Jul-21 10:58:21.849 [main] INFO nextflow.Nextflow - -[nf-core/chipseq] Pipeline completed with errors- Jul-21 10:58:21.862 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=19; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=1d 6h 34m 57s; failedDuration=46.2s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=17; peakCpus=146; peakMemory=876 GB; ] Jul-21 10:58:21.863 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Jul-21 10:58:21.868 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Jul-21 10:58:21.934 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data: [{"cpuUsage":{"mean":80.7,"min":80.7,"q1":80.7,"q2":80.7,"q3":80.7,"max":80.7,"minLabel":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","maxLabel":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","q1Label":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","q2Label":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","q3Label":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)"},"process":"SAMPLESHEET_CHECK","mem":{"mean":1101824,"min":1101824,"q1":1101824,"q2":1101824,"q3":1101824,"max":1101824,"minLabel":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","maxLabel":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","q1Label":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","q2Label":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)","q3Label":"NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK 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shutdown completed (hard=false) Jul-21 10:58:23.024 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye