Jun-04 22:08:41.911 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/riboseq -r 1.1.0 -profile singularity -name riboseq_5 -params-file nf-params.json -resume --extra_ribotricer_detectorfs_args '--phase_score_cutoff 0.2' Jun-04 22:08:42.011 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.4 Jun-04 22:08:42.030 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/mbansal/.nextflow/plugins; core-plugins: nf-amazon@2.9.2,nf-azure@1.10.2,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.3,nf-tower@1.9.3,nf-wave@1.7.4 Jun-04 22:08:42.054 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Jun-04 22:08:42.055 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Jun-04 22:08:42.057 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Jun-04 22:08:42.067 [main] INFO org.pf4j.AbstractPluginManager - No plugins Jun-04 22:08:42.078 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/mbansal/.nextflow/scm Jun-04 22:08:42.918 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/mbansal/.nextflow/assets/nf-core/riboseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/riboseq.git Jun-04 22:08:42.947 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Jun-04 22:08:42.956 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/mbansal/.nextflow/assets/nf-core/riboseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/riboseq.git Jun-04 22:08:44.077 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/mbansal/.nextflow/assets/nf-core/riboseq/nextflow.config Jun-04 22:08:44.080 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/mbansal/.nextflow/assets/nf-core/riboseq/nextflow.config Jun-04 22:08:44.088 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/mbansal/.nextflow/secrets/store.json Jun-04 22:08:44.091 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@5809fa26] - activable => nextflow.secret.LocalSecretsProvider@5809fa26 Jun-04 22:08:44.114 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity` Jun-04 22:08:45.446 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, giga, incliva, ilifu, ki_luria, uge, icr_alma, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, roslin, tes, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, ceci_nic5, ccga_cau, humantechnopole, stjude, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, seattlechildrens, icr_davros, ceres, arm, munin, rosalind, hasta, cfc, uzh, shu_bmrc, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, shifter, biohpc_gen, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, ceci_dragon2, imperial, maestro, software_license, cannon, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, kaust, alliance_canada, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, mssm, sanger, dkfz, bluebear, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, seadragon, crukmi, csiro_petrichor, qmul_apocrita, wave, docker, engaging, gis, hypatia, psmn, eva, unity, cropdiversityhpc, nygc, fgcz, conda, crg, singularity, mpcdf_viper, pe2, self_hosted_runner, tufts, uw_hyak_pedslabs, binac2, debug, genouest, cbe, unsw_katana, gitpod, phoenix, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac, fsu_draco] Jun-04 22:08:45.511 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default Jun-04 22:08:45.512 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/riboseq` [riboseq_5] DSL2 - revision: 235e008eda [1.1.0] Jun-04 22:08:45.515 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.3.0] Jun-04 22:08:45.515 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Jun-04 22:08:45.516 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.3.0] Jun-04 22:08:45.516 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.3.0 Jun-04 22:08:45.562 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.3.0' resolved Jun-04 22:08:45.563 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.3.0' Jun-04 22:08:45.768 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.3.0 Jun-04 22:08:45.806 [main] DEBUG nextflow.Session - Session UUID: 7e1dea40-8b78-4368-b447-157ada473cbd Jun-04 22:08:45.807 [main] DEBUG nextflow.Session - Run name: riboseq_5 Jun-04 22:08:45.807 [main] DEBUG nextflow.Session - Executor pool size: 40 Jun-04 22:08:45.813 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Jun-04 22:08:45.816 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=120; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jun-04 22:08:45.863 [main] DEBUG nextflow.cli.CmdRun - Version: 24.10.4 build 5934 Created: 20-01-2025 16:47 UTC (10:47 CDT) System: Linux 3.10.0-1160.24.1.el7.x86_64 Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.14-internal+0-adhoc..src Encoding: UTF-8 (ANSI_X3.4-1968) Process: 90858@c0225 [172.20.201.225] CPUs: 40 - Mem: 200 GB (199.4 GB) - Swap: 0 (0) Jun-04 22:08:45.907 [main] DEBUG nextflow.Session - Work-dir: /data/project/ding_lab/riboseq/work [gpfs] Jun-04 22:08:45.944 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Jun-04 22:08:45.956 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Jun-04 22:08:45.972 [main] DEBUG nextflow.Session - Observer factory: ValidationObserverFactory Jun-04 22:08:46.035 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Jun-04 22:08:46.043 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 41; maxThreads: 1000 Jun-04 22:08:46.170 [main] DEBUG nextflow.Session - Session start Jun-04 22:08:46.172 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /data/project/ding_lab/riboseq/riboseq/pipeline_info/execution_trace_2025-06-04_22-08-44.txt Jun-04 22:08:46.420 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jun-04 22:08:50.369 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Jun-04 22:08:50.378 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Jun-04 22:08:50.629 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Jun-04 22:08:50.629 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Jun-04 22:08:50.631 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Jun-04 22:08:50.631 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Jun-04 22:08:51.613 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-schema Jun-04 22:08:51.614 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-schema Jun-04 22:08:51.615 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-schema Jun-04 22:08:51.616 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [samplesheetToList:samplesheetToList]; plugin Id: nf-schema Jun-04 22:08:51.803 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/riboseq 1.1.0 ------------------------------------------------------ Input/output options input : samplesheet.csv outdir : riboseq Reference genome options fasta : /data/user/mbansal/Mapping_and_fastq_files/MAPPING_MINIMAP2/reference_genome_files/GRCh38.p13.genome.fa gtf : /data/user/mbansal/Mapping_and_fastq_files/MAPPING_MINIMAP2/reference_genome_files/gencode.v44.annotation.gtf Alignment options min_mapped_reads : 5 Riboseq-specific options extra_ribotricer_detectorfs_args: --phase_score_cutoff 0.2 Generic options trace_report_suffix : 2025-06-04_22-08-44 Core Nextflow options revision : 1.1.0 runName : riboseq_5 containerEngine : singularity launchDir : /data/project/ding_lab/riboseq workDir : /data/project/ding_lab/riboseq/work projectDir : /home/mbansal/.nextflow/assets/nf-core/riboseq userName : mbansal profile : singularity configFiles : /home/mbansal/.nextflow/assets/nf-core/riboseq/nextflow.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ * The pipeline https://doi.org/10.5281/zenodo.10966364 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/riboseq/blob/master/CITATIONS.md Jun-04 22:08:51.806 [main] DEBUG n.validation.ValidationExtension - Starting parameters validation Jun-04 22:08:52.081 [main] DEBUG nextflow.validation.SchemaEvaluator - Started validating /data/project/ding_lab/riboseq/samplesheet.csv Jun-04 22:08:52.139 [main] DEBUG nextflow.validation.SchemaEvaluator - Validation of file 'samplesheet.csv' passed! Jun-04 22:08:52.145 [main] DEBUG n.v.FormatDirectoryPathEvaluator - Cloud blob storage paths are not supported by 'FormatDirectoryPathEvaluator': 's3://ngi-igenomes/igenomes/' Jun-04 22:08:52.147 [main] DEBUG n.validation.ValidationExtension - Finishing parameters validation Jun-04 22:08:52.258 [main] WARN n.validation.SamplesheetConverter - Found the following unidentified headers in /data/project/ding_lab/riboseq/samplesheet.csv: - sample_description - pair - treatment Jun-04 22:08:52.331 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF_FILTER` matches process NFCORE_RIBOSEQ:PREPARE_GENOME:GTF_FILTER Jun-04 22:08:52.342 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.342 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.348 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local Jun-04 22:08:52.355 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=40; memory=200 GB; capacity=40; pollInterval=100ms; dumpInterval=5m Jun-04 22:08:52.357 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) Jun-04 22:08:52.405 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RIBOSEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA Jun-04 22:08:52.409 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA` matches process NFCORE_RIBOSEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA Jun-04 22:08:52.412 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.412 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.432 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Jun-04 22:08:52.434 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_GETCHROMSIZES` matches process NFCORE_RIBOSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Jun-04 22:08:52.439 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.439 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.461 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RIBOSEQ:PREPARE_GENOME:SORTMERNA_INDEX Jun-04 22:08:52.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SORTMERNA_INDEX` matches process NFCORE_RIBOSEQ:PREPARE_GENOME:SORTMERNA_INDEX Jun-04 22:08:52.467 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.467 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RIBOSEQ:PREPARE_GENOME:STAR_GENOMEGENERATE Jun-04 22:08:52.481 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES` matches process NFCORE_RIBOSEQ:PREPARE_GENOME:STAR_GENOMEGENERATE Jun-04 22:08:52.484 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.484 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.524 [main] WARN n.validation.SamplesheetConverter - Found the following unidentified headers in /data/project/ding_lab/riboseq/samplesheet.csv: - sample_description - pair - treatment Jun-04 22:08:52.530 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `salmon_index` -- Initialise it to a default value eg. `params.salmon_index = some_value` Jun-04 22:08:52.530 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `skip_pseudo_alignment` -- Initialise it to a default value eg. `params.skip_pseudo_alignment = some_value` Jun-04 22:08:52.530 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `pseudo_aligner` -- Initialise it to a default value eg. `params.pseudo_aligner = some_value` Jun-04 22:08:52.531 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `sortmerna_index` -- Initialise it to a default value eg. `params.sortmerna_index = some_value` Jun-04 22:08:52.549 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ Jun-04 22:08:52.550 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CAT_FASTQ` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ Jun-04 22:08:52.553 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.553 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.564 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT Jun-04 22:08:52.564 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FQ_LINT` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT Jun-04 22:08:52.567 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.567 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.599 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC Jun-04 22:08:52.601 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC Jun-04 22:08:52.603 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.603 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.617 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE Jun-04 22:08:52.618 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE Jun-04 22:08:52.621 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.621 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.662 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING Jun-04 22:08:52.662 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FQ_LINT` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING Jun-04 22:08:52.663 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FQ_LINT_AFTER_TRIMMING` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING Jun-04 22:08:52.665 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.665 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.679 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX Jun-04 22:08:52.680 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SORTMERNA_INDEX` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX Jun-04 22:08:52.683 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.683 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.687 [main] WARN nextflow.extension.OperatorImpl - The operator `first` is useless when applied to a value channel which returns a single value by definition Jun-04 22:08:52.692 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA Jun-04 22:08:52.693 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA Jun-04 22:08:52.695 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.695 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.704 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA Jun-04 22:08:52.705 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FQ_LINT` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA Jun-04 22:08:52.706 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FQ_LINT_AFTER_SORTMERNA` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA Jun-04 22:08:52.708 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.708 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.726 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX Jun-04 22:08:52.727 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SALMON_INDEX` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX Jun-04 22:08:52.729 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.729 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.735 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE Jun-04 22:08:52.736 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FQ_SUBSAMPLE` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE Jun-04 22:08:52.738 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.738 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.748 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT Jun-04 22:08:52.750 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT Jun-04 22:08:52.753 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.753 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN Jun-04 22:08:52.790 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:STAR_ALIGN` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN Jun-04 22:08:52.794 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.794 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.810 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT Jun-04 22:08:52.811 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_(GEN|TRANSCRIPT)OME:SAMTOOLS_(SORT|INDEX)` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT Jun-04 22:08:52.811 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_(SORT|INDEX)` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT Jun-04 22:08:52.813 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.813 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.823 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX Jun-04 22:08:52.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_(GEN|TRANSCRIPT)OME:SAMTOOLS_(SORT|INDEX)` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX Jun-04 22:08:52.824 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_(SORT|INDEX)` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX Jun-04 22:08:52.826 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.826 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.839 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jun-04 22:08:52.840 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jun-04 22:08:52.842 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.842 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.849 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jun-04 22:08:52.850 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jun-04 22:08:52.852 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.852 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.858 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jun-04 22:08:52.859 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jun-04 22:08:52.861 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.861 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.870 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT Jun-04 22:08:52.871 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_(GEN|TRANSCRIPT)OME:SAMTOOLS_(SORT|INDEX)` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT Jun-04 22:08:52.872 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_(SORT|INDEX)` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT Jun-04 22:08:52.874 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.874 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.881 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX Jun-04 22:08:52.882 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_(GEN|TRANSCRIPT)OME:SAMTOOLS_(SORT|INDEX)` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX Jun-04 22:08:52.882 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_(SORT|INDEX)` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX Jun-04 22:08:52.884 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.884 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.897 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jun-04 22:08:52.898 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jun-04 22:08:52.899 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.899 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.905 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jun-04 22:08:52.906 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jun-04 22:08:52.907 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.907 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.912 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jun-04 22:08:52.915 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NFCORE_RIBOSEQ:RIBOSEQ:.*:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jun-04 22:08:52.917 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.917 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.947 [main] WARN nextflow.extension.OperatorImpl - The operator `first` is useless when applied to a value channel which returns a single value by definition Jun-04 22:08:52.953 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ Jun-04 22:08:52.953 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:RIBOTISH_QUALITY` matches process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ Jun-04 22:08:52.956 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.956 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.970 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL Jun-04 22:08:52.972 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:RIBOTISH_PREDICT_INDIVIDUAL` matches process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL Jun-04 22:08:52.974 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.974 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.986 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL Jun-04 22:08:52.988 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:RIBOTISH_PREDICT_ALL` matches process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL Jun-04 22:08:52.990 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:52.990 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:52.999 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_PREPAREORFS Jun-04 22:08:53.000 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:RIBOTRICER_PREPAREORFS` matches process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_PREPAREORFS Jun-04 22:08:53.002 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.002 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.012 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS Jun-04 22:08:53.013 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:RIBOTRICER_DETECTORFS` matches process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS Jun-04 22:08:53.016 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.016 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT Jun-04 22:08:53.036 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SALMON_QUANT` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT Jun-04 22:08:53.038 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.038 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE Jun-04 22:08:53.054 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE Jun-04 22:08:53.056 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.056 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.072 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT Jun-04 22:08:53.073 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT Jun-04 22:08:53.076 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.076 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.092 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE Jun-04 22:08:53.094 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE Jun-04 22:08:53.094 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_GENE` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE Jun-04 22:08:53.096 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.096 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.105 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED Jun-04 22:08:53.107 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED Jun-04 22:08:53.107 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED Jun-04 22:08:53.109 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.109 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.117 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED Jun-04 22:08:53.118 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED Jun-04 22:08:53.119 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_GENE_SCALED` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED Jun-04 22:08:53.120 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.120 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.128 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT Jun-04 22:08:53.130 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_.*` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT Jun-04 22:08:53.130 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT` matches process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT Jun-04 22:08:53.131 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.132 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.213 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RIBOSEQ:RIBOSEQ:MULTIQC Jun-04 22:08:53.214 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_RIBOSEQ:RIBOSEQ:MULTIQC Jun-04 22:08:53.216 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null Jun-04 22:08:53.216 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' Jun-04 22:08:53.232 [main] DEBUG nextflow.Session - Config process names validation disabled as requested Jun-04 22:08:53.233 [main] DEBUG nextflow.Session - Igniting dataflow network (84) Jun-04 22:08:53.234 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:PREPARE_GENOME:GTF_FILTER Jun-04 22:08:53.234 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA Jun-04 22:08:53.234 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES Jun-04 22:08:53.234 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:PREPARE_GENOME:SORTMERNA_INDEX Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:PREPARE_GENOME:STAR_GENOMEGENERATE Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX Jun-04 22:08:53.235 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE Jun-04 22:08:53.236 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT Jun-04 22:08:53.237 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_PREPAREORFS Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED Jun-04 22:08:53.238 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT Jun-04 22:08:53.244 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RIBOSEQ:RIBOSEQ:MULTIQC Jun-04 22:08:53.245 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_d3865926248d0c08: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_align_star/../bam_sort_stats_samtools/../bam_stats_samtools/../../../modules/nf-core/samtools/stats/main.nf Script_700a4742a1f56b73: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_trimgalore/main.nf Script_cdbce3e23a8f89e8: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/bam_dedup_umi/../bam_dedup_stats_samtools_umicollapse/../bam_stats_samtools/main.nf Script_b4e3753ed1e86538: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../modules/nf-core/ribotish/predict/main.nf Script_a780234b47eb3af3: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/gunzip/main.nf Script_436714e6cce8064e: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/bam_dedup_umi/main.nf Script_4133e0a81c0b1738: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_align_star/main.nf Script_0fdb2e5f8575be0c: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../modules/nf-core/multiqc/main.nf Script_3ff1656b1d66c1f2: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_align_star/../bam_sort_stats_samtools/../../../modules/nf-core/samtools/index/main.nf Script_07de1df82deeb8cc: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/local/gtf_filter/main.nf Script_114061501d4048bf: /home/mbansal/.nextflow/assets/nf-core/riboseq/main.nf Script_a63acce74c0c0ffc: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/star/genomegenerate/main.nf Script_61f4f72de66b39fa: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/bam_dedup_umi/../bam_dedup_stats_samtools_umicollapse/main.nf Script_223ca400878df5b0: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/untar/main.nf Script_e2f971e92b77b671: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/main.nf Script_7b33c5cb92303970: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/main.nf Script_8539cabf2246c13c: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../../../modules/nf-core/bbmap/bbsplit/main.nf Script_ad119ddb6089cee6: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/local/star_genomegenerate_igenomes/main.nf Script_59101990e865c327: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/../../../modules/nf-core/umitools/dedup/main.nf Script_916cff5dd7267826: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/local/utils_nfcore_riboseq_pipeline/main.nf Script_b4163cee6a6b2681: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_trimgalore/../../../modules/nf-core/umitools/extract/main.nf Script_01998db898cee87d: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../modules/nf-core/ribotish/quality/main.nf Script_2cd3960e599fb6c8: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/bam_dedup_umi/../bam_sort_stats_samtools/../bam_stats_samtools/../../../modules/nf-core/samtools/idxstats/main.nf Script_1adca4cb4e6fb5ea: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf Script_bac6d352d496d867: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/rsem/preparereference/main.nf Script_78bf8b6ebf2410dd: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/custom/catadditionalfasta/main.nf Script_d95de3a65f05cb9b: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/kallisto/quant/main.nf Script_b666edf0129ec7fc: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/gffread/main.nf Script_a7567bced3b57507: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../modules/nf-core/ribotricer/prepareorfs/main.nf Script_22e881f90cabfe1d: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/custom/getchromsizes/main.nf Script_869203474861dfb0: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../modules/nf-core/anota2seq/anota2seqrun/main.nf Script_215a636da7ab24a2: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/utils_nfcore_riboseq_pipeline/../../nf-core/utils_nfschema_plugin/main.nf Script_e450b5a5a70fe0a3: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/bam_dedup_umi/../bam_dedup_stats_samtools_umicollapse/../../../modules/nf-core/umicollapse/main.nf Script_5c4e8d4051efa81e: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/local/utils_nfcore_riboseq_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf Script_6012db1a2adb3e63: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/summarizedexperiment/summarizedexperiment/main.nf Script_de1c7c124fa4c7b4: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/bam_dedup_umi/../../../modules/nf-core/samtools/sort/main.nf Script_2580806872fee805: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../../../modules/nf-core/fq/lint/main.nf Script_9f6ce129b29ed4a5: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_fastp/../../../modules/nf-core/fastp/main.nf Script_c8f3946cfec071c8: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../modules/nf-core/ribotricer/detectorfs/main.nf Script_7a66424f9cfe9c28: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../../../modules/nf-core/cat/fastq/main.nf Script_3fe75c83449750cf: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/salmon/index/main.nf Script_4ab78e6cd625daeb: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/local/gtf2bed/main.nf Script_498db87a6d4f03d8: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_align_star/../bam_sort_stats_samtools/../bam_stats_samtools/../../../modules/nf-core/samtools/flagstat/main.nf Script_312efecf0c399931: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf Script_d09a57bae36c5a8c: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/salmon/quant/main.nf Script_4f612cfd8c52e8cd: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/local/utils_nfcore_riboseq_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf Script_d819f6ef17f98d2c: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_trimgalore/../../../modules/nf-core/trimgalore/main.nf Script_da05a45d4fc5617e: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/nf-core/sortmerna/main.nf Script_04d488c7ab8c434e: /home/mbansal/.nextflow/assets/nf-core/riboseq/./subworkflows/local/prepare_genome/../../../modules/local/preprocess_transcripts_fasta_gencode/main.nf Script_d203577fd573143e: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_fastp/main.nf Script_c3f4bd3b3e600606: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/quantify_pseudo_alignment/main.nf Script_128cb4fde5e21aab: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/custom/tx2gene/main.nf Script_2b72a5be5c8fe209: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/quantify_pseudo_alignment/../../../modules/nf-core/tximeta/tximport/main.nf Script_dc41886bdbd95b0b: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_fastqc_umitools_fastp/../../../modules/nf-core/fastqc/main.nf Script_8ea3feb9c15d5fda: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_subsample_fq_salmon/../../../modules/nf-core/fq/subsample/main.nf Script_e76b9210f32f34ec: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../modules/nf-core/umitools/prepareforrsem/main.nf Script_65fc7d2789b86134: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_align_star/../../../modules/nf-core/star/align/main.nf Script_f1f53abfc1403f76: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/../fastq_subsample_fq_salmon/main.nf Script_2ebe1d1a775a7432: /home/mbansal/.nextflow/assets/nf-core/riboseq/./workflows/riboseq/../../subworkflows/nf-core/fastq_align_star/../bam_sort_stats_samtools/main.nf Jun-04 22:08:53.245 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Jun-04 22:08:53.245 [main] DEBUG nextflow.Session - Session await Jun-04 22:08:53.302 [Actor Thread 25] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data; path=/data/project/ding_lab/riboseq/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-c2-c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975-data.img Jun-04 22:08:53.302 [Actor Thread 34] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/python:3.9--1; path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-python-3.9--1.img Jun-04 22:08:53.302 [Actor Thread 28] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0; path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-samtools-1.21--h50ea8bc_0.img Jun-04 22:08:53.316 [Actor Thread 27] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/mbansal/.nextflow/assets/nf-core/riboseq/bin/filter_gtf.py Jun-04 22:08:53.402 [Actor Thread 37] INFO nextflow.processor.TaskProcessor - [24/2067e7] Cached process > NFCORE_RIBOSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (GRCh38.p13.genome.fa) Jun-04 22:08:53.402 [Actor Thread 21] INFO nextflow.processor.TaskProcessor - [b2/3f8ecf] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (SNORD133_knockout_2) Jun-04 22:08:53.402 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [cc/973cb3] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (SNORD97_knockout_2) Jun-04 22:08:53.402 [Actor Thread 40] INFO nextflow.processor.TaskProcessor - [e6/035507] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (SNORD133_knockout_1) Jun-04 22:08:53.402 [Actor Thread 22] INFO nextflow.processor.TaskProcessor - [e6/fcf09b] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (SNORD97_knockout_1) Jun-04 22:08:53.402 [Actor Thread 27] INFO nextflow.processor.TaskProcessor - [cc/176183] Cached process > NFCORE_RIBOSEQ:PREPARE_GENOME:GTF_FILTER (GRCh38.p13.genome.fa) Jun-04 22:08:53.407 [Actor Thread 24] INFO nextflow.processor.TaskProcessor - [00/40f94b] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_1) Jun-04 22:08:53.407 [Actor Thread 23] INFO nextflow.processor.TaskProcessor - [9c/236b45] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (SNORD97_133_double_knockout_2) Jun-04 22:08:53.421 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [7c/421a85] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_2) Jun-04 22:08:53.425 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [20/d5d48c] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (SNORD97_133_double_knockout_1) Jun-04 22:08:53.461 [Actor Thread 45] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fq:0.12.0--h9ee0642_0; path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-fq-0.12.0--h9ee0642_0.img Jun-04 22:08:53.464 [Actor Thread 7] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0; path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b-64aad4a4e144878400649e71f42105311be7ed87-0.img Jun-04 22:08:53.465 [Actor Thread 3] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/ribotricer:1.3.3--pyhdfd78af_0; path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-ribotricer-1.3.3--pyhdfd78af_0.img Jun-04 22:08:53.465 [Actor Thread 7] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9becad054093ad4083a961d12733f2a742e11728fe9aa815d678b882b3ede520/data; path=/data/project/ding_lab/riboseq/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-9b-9becad054093ad4083a961d12733f2a742e11728fe9aa815d678b882b3ede520-data.img Jun-04 22:08:53.466 [Actor Thread 3] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0; path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img Jun-04 22:08:53.483 [Actor Thread 44] INFO nextflow.processor.TaskProcessor - [62/34ac61] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (SNORD97_knockout_1) Jun-04 22:08:53.498 [Actor Thread 1] INFO nextflow.processor.TaskProcessor - [87/a30173] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (SNORD97_knockout_2) Jun-04 22:08:53.503 [Actor Thread 11] INFO nextflow.processor.TaskProcessor - [53/e05d31] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_PREPAREORFS (null) Jun-04 22:08:53.504 [Actor Thread 5] INFO nextflow.processor.TaskProcessor - [8b/c1dabe] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (SNORD97_133_double_knockout_2) Jun-04 22:08:53.508 [Actor Thread 10] INFO nextflow.processor.TaskProcessor - [90/10fd19] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (SNORD133_knockout_2) Jun-04 22:08:53.509 [Actor Thread 11] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=120; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jun-04 22:08:53.509 [Actor Thread 18] INFO nextflow.processor.TaskProcessor - [32/5592d7] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (SNORD133_knockout_1) Jun-04 22:08:53.523 [Actor Thread 48] INFO nextflow.processor.TaskProcessor - [18/8e3fc4] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_2) Jun-04 22:08:53.527 [Actor Thread 51] INFO nextflow.processor.TaskProcessor - [ff/f9eb50] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_1) Jun-04 22:08:53.533 [Actor Thread 24] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/101ea47973178f85ff66a34de6a7462aaf99d947d3924c27ce8a2d5a63009065/data; path=/data/project/ding_lab/riboseq/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-10-101ea47973178f85ff66a34de6a7462aaf99d947d3924c27ce8a2d5a63009065-data.img Jun-04 22:08:53.536 [Actor Thread 46] INFO nextflow.processor.TaskProcessor - [53/4bae5c] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SNORD133_knockout_1) Jun-04 22:08:53.538 [Actor Thread 52] INFO nextflow.processor.TaskProcessor - [36/b64c3f] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SNORD97_knockout_1) Jun-04 22:08:53.539 [Actor Thread 50] INFO nextflow.processor.TaskProcessor - [83/81ecb7] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SNORD97_knockout_2) Jun-04 22:08:53.540 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [45/514efd] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SNORD97_133_double_knockout_1) Jun-04 22:08:53.541 [Actor Thread 12] INFO nextflow.processor.TaskProcessor - [e6/32882c] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SNORD97_133_double_knockout_1) Jun-04 22:08:53.541 [Actor Thread 43] INFO nextflow.processor.TaskProcessor - [93/8058c2] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SNORD97_133_double_knockout_2) Jun-04 22:08:53.542 [Actor Thread 9] INFO nextflow.processor.TaskProcessor - [7a/62400d] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SNORD133_knockout_2) Jun-04 22:08:53.542 [Actor Thread 45] INFO nextflow.processor.TaskProcessor - [92/5f03ac] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_2) Jun-04 22:08:53.542 [Actor Thread 13] INFO nextflow.processor.TaskProcessor - [d0/fe276c] Cached process > NFCORE_RIBOSEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/GRCh38.p13.genome.fa) Jun-04 22:08:53.547 [Actor Thread 32] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.002 s; total time: 0.002 s Jun-04 22:08:53.547 [Actor Thread 14] INFO nextflow.processor.TaskProcessor - [1c/1fadd5] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_1) Jun-04 22:08:53.548 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [cb/c26657] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (SNORD97_133_double_knockout_1) Jun-04 22:08:53.548 [Actor Thread 26] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 16; slices: 1; internal sort time: 0.011 s; external sort time: 0.003 s; total time: 0.014 s Jun-04 22:08:53.551 [Actor Thread 32] DEBUG nextflow.file.FileCollector - >> temp file exists? false Jun-04 22:08:53.552 [Actor Thread 32] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /data/project/ding_lab/riboseq/work/collect-file/9c2e634ea2ae05fbd0d96bd41881cd90 Jun-04 22:08:53.552 [Actor Thread 41] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.001 s; total time: 0.001 s Jun-04 22:08:53.552 [Actor Thread 26] DEBUG nextflow.file.FileCollector - >> temp file exists? true Jun-04 22:08:53.552 [Actor Thread 41] DEBUG nextflow.file.FileCollector - >> temp file exists? false Jun-04 22:08:53.552 [Actor Thread 41] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /data/project/ding_lab/riboseq/work/collect-file/14c7cb1cd3c55f14929a1e5979a08b41 Jun-04 22:08:53.553 [Actor Thread 42] INFO nextflow.processor.TaskProcessor - [54/96ade3] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_2) Jun-04 22:08:53.555 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [54/ec00ba] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SNORD133_knockout_1) Jun-04 22:08:53.557 [Actor Thread 8] INFO nextflow.processor.TaskProcessor - [ec/27c422] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SNORD133_knockout_2) Jun-04 22:08:53.559 [Actor Thread 26] DEBUG nextflow.file.FileCollector - Retrieved cached collect-files from: /data/project/ding_lab/riboseq/work/collect-file/98fc19740eff6872f0b76860f82b6c5e Jun-04 22:08:53.562 [Actor Thread 28] INFO nextflow.processor.TaskProcessor - [7d/4f8c0c] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SNORD97_knockout_2) Jun-04 22:08:53.564 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [17/7bf8e8] Cached process > NFCORE_RIBOSEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (GRCh38.p13.genome.fa) Jun-04 22:08:53.564 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [3c/c7f0ac] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SNORD97_knockout_1) Jun-04 22:08:53.566 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [fe/90a314] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SNORD97_133_double_knockout_2) Jun-04 22:08:53.571 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [d1/3e2df6] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_1) Jun-04 22:08:53.574 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:08:53.574 [Actor Thread 37] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:08:53.576 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:08:53.577 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:08:53.577 [Actor Thread 26] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/local/nxf-8879151502005133957 Jun-04 22:08:53.577 [Actor Thread 2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:08:53.579 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:08:53.581 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:08:53.582 [Actor Thread 25] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:08:53.583 [Actor Thread 42] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:08:53.590 [Actor Thread 41] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /data/project/ding_lab/riboseq/work/collect-file/14c7cb1cd3c55f14929a1e5979a08b41 Jun-04 22:08:53.594 [Actor Thread 32] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /data/project/ding_lab/riboseq/work/collect-file/9c2e634ea2ae05fbd0d96bd41881cd90 Jun-04 22:08:53.595 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [05/df2dd1] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (SNORD97_133_double_knockout_1) Jun-04 22:08:53.596 [Actor Thread 41] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/local/nxf-11177163425250777546 Jun-04 22:08:53.597 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [d4/8a9f00] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_1) Jun-04 22:08:53.615 [Actor Thread 35] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null Jun-04 22:08:53.616 [Actor Thread 32] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/local/nxf-5834939972182786788 Jun-04 22:08:53.622 [Actor Thread 30] INFO nextflow.processor.TaskProcessor - [79/b0bbe4] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (SNORD97_133_double_knockout_2) Jun-04 22:08:53.624 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [db/9ea344] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (SNORD97_knockout_1) Jun-04 22:08:53.625 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [c6/f30f92] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (SNORD97_knockout_2) Jun-04 22:08:53.629 [Actor Thread 50] INFO nextflow.processor.TaskProcessor - [d3/e4ab6b] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (SNORD133_knockout_2) Jun-04 22:08:53.631 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [e5/4574ad] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (SNORD133_knockout_1) Jun-04 22:08:53.635 [Actor Thread 28] INFO nextflow.processor.TaskProcessor - [82/d92aed] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_2) Jun-04 22:08:57.892 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5.8s-database-id98.fasta at /data/project/ding_lab/riboseq/work/stage-7e1dea40-8b78-4368-b447-157ada473cbd/35/fc0e8e91facfa037b03406f4acc452/rfam-5.8s-database-id98.fasta Jun-04 22:08:57.893 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-arc-16s-id95.fasta at /data/project/ding_lab/riboseq/work/stage-7e1dea40-8b78-4368-b447-157ada473cbd/38/4d50e33720849508576434cbb5652e/silva-arc-16s-id95.fasta Jun-04 22:08:57.893 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-arc-23s-id98.fasta at /data/project/ding_lab/riboseq/work/stage-7e1dea40-8b78-4368-b447-157ada473cbd/98/2a6fed4d7e0e858714096af0d9960a/silva-arc-23s-id98.fasta Jun-04 22:08:57.893 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5s-database-id98.fasta at /data/project/ding_lab/riboseq/work/stage-7e1dea40-8b78-4368-b447-157ada473cbd/92/cbce52a5d8e8b3a56f5e6d233ad8f5/rfam-5s-database-id98.fasta Jun-04 22:08:57.894 [FileTransfer-5] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-bac-16s-id90.fasta at /data/project/ding_lab/riboseq/work/stage-7e1dea40-8b78-4368-b447-157ada473cbd/c6/88da523e2af4add02a92143fbd07f9/silva-bac-16s-id90.fasta Jun-04 22:08:57.894 [FileTransfer-6] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-bac-23s-id98.fasta at /data/project/ding_lab/riboseq/work/stage-7e1dea40-8b78-4368-b447-157ada473cbd/77/8e97e9060b692b4733e87e5e4fb19a/silva-bac-23s-id98.fasta Jun-04 22:08:57.895 [FileTransfer-7] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-euk-18s-id95.fasta at /data/project/ding_lab/riboseq/work/stage-7e1dea40-8b78-4368-b447-157ada473cbd/3c/ba5cbff456994917e56c67bc7b3f3f/silva-euk-18s-id95.fasta Jun-04 22:08:57.895 [FileTransfer-8] DEBUG nextflow.file.FilePorter - Local cache found for foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-euk-28s-id98.fasta at /data/project/ding_lab/riboseq/work/stage-7e1dea40-8b78-4368-b447-157ada473cbd/a5/96f63c0f0079e654c4f4d7a42eeb3b/silva-euk-28s-id98.fasta Jun-04 22:08:57.899 [Actor Thread 7] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0; path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-sortmerna-4.3.6--h9ee0642_0.img Jun-04 22:08:57.914 [Actor Thread 29] INFO nextflow.processor.TaskProcessor - [17/83feaf] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX ([]) Jun-04 22:08:57.914 [Actor Thread 28] INFO nextflow.processor.TaskProcessor - [4f/e23c8c] Cached process > NFCORE_RIBOSEQ:PREPARE_GENOME:SORTMERNA_INDEX ([]) Jun-04 22:08:57.915 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:08:57.915 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:PREPARE_GENOME:SORTMERNA_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:08:57.915 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:08:57.915 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:PREPARE_GENOME:SORTMERNA_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.355 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [8b/efd070] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (SNORD97_133_double_knockout_2) Jun-04 22:09:03.357 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [b3/200170] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (SNORD133_knockout_2) Jun-04 22:09:03.357 [Actor Thread 8] INFO nextflow.processor.TaskProcessor - [47/177117] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (SNORD97_133_double_knockout_1) Jun-04 22:09:03.358 [Actor Thread 41] INFO nextflow.processor.TaskProcessor - [90/9c605b] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (SNORD97_knockout_1) Jun-04 22:09:03.358 [Actor Thread 42] INFO nextflow.processor.TaskProcessor - [d2/13439e] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (SNORD97_knockout_2) Jun-04 22:09:03.359 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [c3/18249e] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (WT_2) Jun-04 22:09:03.360 [Actor Thread 32] INFO nextflow.processor.TaskProcessor - [e3/d986e9] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (WT_1) Jun-04 22:09:03.361 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [a6/54e2c4] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (SNORD133_knockout_1) Jun-04 22:09:03.387 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [d4/e73345] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA (SNORD97_knockout_2) Jun-04 22:09:03.388 [Actor Thread 37] INFO nextflow.processor.TaskProcessor - [5b/a6bad2] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA (SNORD133_knockout_2) Jun-04 22:09:03.390 [Actor Thread 2] INFO nextflow.processor.TaskProcessor - [3c/6ce049] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA (SNORD97_133_double_knockout_1) Jun-04 22:09:03.391 [Actor Thread 12] INFO nextflow.processor.TaskProcessor - [44/994b3f] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA (SNORD97_133_double_knockout_2) Jun-04 22:09:03.393 [Actor Thread 42] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 1 FASTQ files Jun-04 22:09:03.393 [Actor Thread 39] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 1 FASTQ files Jun-04 22:09:03.393 [Actor Thread 29] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 1 FASTQ files Jun-04 22:09:03.393 [Actor Thread 28] INFO nextflow.processor.TaskProcessor - [69/4bff60] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA (WT_2) Jun-04 22:09:03.394 [Actor Thread 38] INFO nextflow.processor.TaskProcessor - [90/d568c5] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA (SNORD97_knockout_1) Jun-04 22:09:03.394 [Actor Thread 50] INFO nextflow.processor.TaskProcessor - [09/b60b0e] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA (SNORD133_knockout_1) Jun-04 22:09:03.394 [Actor Thread 32] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 1 FASTQ files Jun-04 22:09:03.396 [Actor Thread 47] INFO nextflow.processor.TaskProcessor - [9b/1b3068] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_SORTMERNA (WT_1) Jun-04 22:09:03.396 [Actor Thread 28] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2; path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-salmon-1.10.3--h6dccd9a_2.img Jun-04 22:09:03.396 [Actor Thread 26] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 1 FASTQ files Jun-04 22:09:03.397 [Actor Thread 37] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 1 FASTQ files Jun-04 22:09:03.398 [Actor Thread 8] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 1 FASTQ files Jun-04 22:09:03.399 [Actor Thread 35] DEBUG nextflow.Nextflow - FQ/SUBSAMPLE found 1 FASTQ files Jun-04 22:09:03.407 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [2c/499b77] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa) Jun-04 22:09:03.424 [Actor Thread 29] INFO nextflow.processor.TaskProcessor - [4f/44c5d0] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (SNORD97_133_double_knockout_1) Jun-04 22:09:03.427 [Actor Thread 39] INFO nextflow.processor.TaskProcessor - [b0/05bffb] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (SNORD97_knockout_2) Jun-04 22:09:03.428 [Actor Thread 42] INFO nextflow.processor.TaskProcessor - [1d/b2c4ce] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (SNORD133_knockout_2) Jun-04 22:09:03.429 [Actor Thread 26] INFO nextflow.processor.TaskProcessor - [e9/041f4c] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_2) Jun-04 22:09:03.431 [Actor Thread 32] INFO nextflow.processor.TaskProcessor - [31/127b82] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (SNORD97_133_double_knockout_2) Jun-04 22:09:03.434 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [e1/e25e99] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_1) Jun-04 22:09:03.435 [Actor Thread 37] INFO nextflow.processor.TaskProcessor - [41/013f6b] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (SNORD97_knockout_1) Jun-04 22:09:03.435 [Actor Thread 8] INFO nextflow.processor.TaskProcessor - [96/e2d5f1] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (SNORD133_knockout_1) Jun-04 22:09:03.451 [Actor Thread 50] INFO nextflow.processor.TaskProcessor - [12/905e63] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (SNORD97_133_double_knockout_1) Jun-04 22:09:03.452 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [b2/2c3ff5] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_2) Jun-04 22:09:03.455 [Actor Thread 39] INFO nextflow.processor.TaskProcessor - [ce/efe70b] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (SNORD133_knockout_2) Jun-04 22:09:03.455 [Actor Thread 29] INFO nextflow.processor.TaskProcessor - [c2/3310a5] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (SNORD97_knockout_2) Jun-04 22:09:03.457 [Actor Thread 38] INFO nextflow.processor.TaskProcessor - [8c/07d24c] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (SNORD97_133_double_knockout_2) Jun-04 22:09:03.461 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [58/c73782] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (SNORD97_knockout_1) Jun-04 22:09:03.462 [Actor Thread 42] INFO nextflow.processor.TaskProcessor - [eb/27e8c8] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (SNORD133_knockout_1) Jun-04 22:09:03.462 [Actor Thread 26] INFO nextflow.processor.TaskProcessor - [15/ffd10f] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_1) Jun-04 22:09:03.490 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (6)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/4f/937d6581db1a29e1695eb6cd9b12e1/SNORD97_knockout_1.sortedByCoord.out.bam` (pattern: `SNORD97_knockout_1.sortedByCoord.out.bam`) Jun-04 22:09:03.491 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (6)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/4f/937d6581db1a29e1695eb6cd9b12e1/SNORD97_knockout_1.Aligned.sortedByCoord.out.bam` (pattern: `SNORD97_knockout_1.Aligned.sortedByCoord.out.bam`) Jun-04 22:09:03.503 [Actor Thread 8] INFO nextflow.processor.TaskProcessor - [4f/937d65] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_knockout_1) Jun-04 22:09:03.504 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (3)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/bb/e5fb2e1df13f6ddf1b49b0eac11692/SNORD133_knockout_2.sortedByCoord.out.bam` (pattern: `SNORD133_knockout_2.sortedByCoord.out.bam`) Jun-04 22:09:03.504 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (3)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/bb/e5fb2e1df13f6ddf1b49b0eac11692/SNORD133_knockout_2.Aligned.sortedByCoord.out.bam` (pattern: `SNORD133_knockout_2.Aligned.sortedByCoord.out.bam`) Jun-04 22:09:03.505 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (8)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/c2/0b3a01ed196110b84556b4877317d3/WT_1.sortedByCoord.out.bam` (pattern: `WT_1.sortedByCoord.out.bam`) Jun-04 22:09:03.505 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (1)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/05/0e3b439716a1d114e98a0fd7e3ab1b/SNORD97_133_double_knockout_1.sortedByCoord.out.bam` (pattern: `SNORD97_133_double_knockout_1.sortedByCoord.out.bam`) Jun-04 22:09:03.505 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (7)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/ac/b300656ab459eb986c4224eef93e08/SNORD133_knockout_1.sortedByCoord.out.bam` (pattern: `SNORD133_knockout_1.sortedByCoord.out.bam`) Jun-04 22:09:03.505 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (2)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/8c/17d592410e9c29a080ca7becd81b46/WT_2.sortedByCoord.out.bam` (pattern: `WT_2.sortedByCoord.out.bam`) Jun-04 22:09:03.505 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (7)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/ac/b300656ab459eb986c4224eef93e08/SNORD133_knockout_1.Aligned.sortedByCoord.out.bam` (pattern: `SNORD133_knockout_1.Aligned.sortedByCoord.out.bam`) Jun-04 22:09:03.505 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (8)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/c2/0b3a01ed196110b84556b4877317d3/WT_1.Aligned.sortedByCoord.out.bam` (pattern: `WT_1.Aligned.sortedByCoord.out.bam`) Jun-04 22:09:03.505 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (1)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/05/0e3b439716a1d114e98a0fd7e3ab1b/SNORD97_133_double_knockout_1.Aligned.sortedByCoord.out.bam` (pattern: `SNORD97_133_double_knockout_1.Aligned.sortedByCoord.out.bam`) Jun-04 22:09:03.505 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (2)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/8c/17d592410e9c29a080ca7becd81b46/WT_2.Aligned.sortedByCoord.out.bam` (pattern: `WT_2.Aligned.sortedByCoord.out.bam`) Jun-04 22:09:03.507 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-04 22:09:03.507 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-04 22:09:03.508 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-04 22:09:03.508 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-04 22:09:03.508 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-04 22:09:03.508 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-04 22:09:03.508 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-04 22:09:03.508 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-04 22:09:03.508 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-04 22:09:03.517 [Actor Thread 29] INFO nextflow.processor.TaskProcessor - [bb/e5fb2e] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD133_knockout_2) Jun-04 22:09:03.520 [Actor Thread 26] INFO nextflow.processor.TaskProcessor - [ac/b30065] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD133_knockout_1) Jun-04 22:09:03.520 [Actor Thread 36] INFO nextflow.processor.TaskProcessor - [c2/0b3a01] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (WT_1) Jun-04 22:09:03.520 [Actor Thread 39] INFO nextflow.processor.TaskProcessor - [05/0e3b43] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_133_double_knockout_1) Jun-04 22:09:03.521 [Actor Thread 7] INFO nextflow.processor.TaskProcessor - [8c/17d592] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (WT_2) Jun-04 22:09:03.521 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-04 22:09:03.521 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-04 22:09:03.521 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-04 22:09:03.521 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-04 22:09:03.521 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-04 22:09:03.522 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-04 22:09:03.522 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-04 22:09:03.522 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-04 22:09:03.522 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-04 22:09:03.525 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-04 22:09:03.525 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-04 22:09:03.525 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-04 22:09:03.525 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-04 22:09:03.525 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-04 22:09:03.525 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-04 22:09:03.525 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-04 22:09:03.526 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-04 22:09:03.526 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-04 22:09:03.529 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-04 22:09:03.529 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-04 22:09:03.529 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-04 22:09:03.529 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-04 22:09:03.530 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-04 22:09:03.530 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-04 22:09:03.530 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-04 22:09:03.530 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-04 22:09:03.530 [Actor Thread 36] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-04 22:09:03.532 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:03.533 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-04 22:09:03.533 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-04 22:09:03.533 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-04 22:09:03.533 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-04 22:09:03.533 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-04 22:09:03.533 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-04 22:09:03.533 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-04 22:09:03.533 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-04 22:09:03.533 [Actor Thread 26] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-04 22:09:03.535 [Task submitter] INFO nextflow.Session - [4b/1530e5] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_knockout_2) Jun-04 22:09:03.538 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-04 22:09:03.538 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-04 22:09:03.538 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-04 22:09:03.538 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-04 22:09:03.539 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-04 22:09:03.539 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-04 22:09:03.539 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-04 22:09:03.539 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-04 22:09:03.539 [Actor Thread 12] INFO nextflow.processor.TaskProcessor - [0f/586bc3] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD97_knockout_1) Jun-04 22:09:03.539 [Actor Thread 7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-04 22:09:03.539 [Actor Thread 28] INFO nextflow.processor.TaskProcessor - [60/a59abe] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_knockout_1) Jun-04 22:09:03.540 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [63/088917] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_knockout_1) Jun-04 22:09:03.542 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.543 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.543 [Actor Thread 12] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:03.543 [Actor Thread 35] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.544 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.544 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.544 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:03.548 [Actor Thread 19] INFO nextflow.processor.TaskProcessor - [31/ae5f40] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_1) Jun-04 22:09:03.550 [Actor Thread 47] INFO nextflow.processor.TaskProcessor - [e8/34fef9] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_1) Jun-04 22:09:03.550 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.550 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.550 [Actor Thread 19] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:03.552 [Actor Thread 47] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.552 [Actor Thread 47] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.552 [Actor Thread 47] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:03.554 [Actor Thread 6] INFO nextflow.processor.TaskProcessor - [6a/e5594f] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_133_double_knockout_1) Jun-04 22:09:03.554 [Actor Thread 41] INFO nextflow.processor.TaskProcessor - [f0/ea3800] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (WT_1) Jun-04 22:09:03.556 [Actor Thread 6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.556 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:03.556 [Actor Thread 41] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.557 [Actor Thread 41] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.557 [Actor Thread 41] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:03.557 [Task submitter] INFO nextflow.Session - [69/8e979b] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_133_double_knockout_2) Jun-04 22:09:03.557 [Actor Thread 50] INFO nextflow.processor.TaskProcessor - [bb/03945a] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (WT_1) Jun-04 22:09:03.557 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [cb/3afb19] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD133_knockout_1) Jun-04 22:09:03.559 [Actor Thread 50] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.559 [Actor Thread 50] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.559 [Actor Thread 15] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.559 [Actor Thread 50] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:03.559 [Actor Thread 15] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.559 [Actor Thread 15] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:03.561 [Actor Thread 42] INFO nextflow.processor.TaskProcessor - [36/7fe558] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD133_knockout_1) Jun-04 22:09:03.561 [Actor Thread 25] INFO nextflow.processor.TaskProcessor - [cb/1a6d33] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD133_knockout_1) Jun-04 22:09:03.561 [Actor Thread 20] INFO nextflow.processor.TaskProcessor - [10/9cc11f] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_1) Jun-04 22:09:03.563 [Actor Thread 42] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.563 [Actor Thread 42] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.563 [Actor Thread 20] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.563 [Actor Thread 42] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:03.564 [Actor Thread 29] INFO nextflow.processor.TaskProcessor - [0f/71fd54] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD97_knockout_1) Jun-04 22:09:03.564 [Actor Thread 25] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.565 [Actor Thread 28] INFO nextflow.processor.TaskProcessor - [81/96777f] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD97_133_double_knockout_1) Jun-04 22:09:03.566 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.566 [Actor Thread 29] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.567 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.567 [Actor Thread 28] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.568 [Actor Thread 38] INFO nextflow.processor.TaskProcessor - [f8/ba8568] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD97_knockout_1) Jun-04 22:09:03.569 [Actor Thread 38] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.569 [Actor Thread 38] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.572 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:03.572 [Task submitter] INFO nextflow.Session - [80/6610e2] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD133_knockout_2) Jun-04 22:09:03.574 [Actor Thread 15] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/ribotish:0.2.7--pyhdfd78af_0; path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-ribotish-0.2.7--pyhdfd78af_0.img Jun-04 22:09:03.574 [Actor Thread 39] INFO nextflow.processor.TaskProcessor - [63/040eea] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (WT_1) Jun-04 22:09:03.575 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.576 [Actor Thread 39] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.580 [Actor Thread 8] INFO nextflow.processor.TaskProcessor - [3e/da3928] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (WT_1) Jun-04 22:09:03.580 [Actor Thread 47] INFO nextflow.processor.TaskProcessor - [6d/1fb17e] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD133_knockout_1) Jun-04 22:09:03.581 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:03.581 [Task submitter] INFO nextflow.Session - [96/ba62fe] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD97_133_double_knockout_1) Jun-04 22:09:03.581 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.581 [Actor Thread 8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.582 [Actor Thread 47] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.582 [Actor Thread 47] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.584 [Actor Thread 35] INFO nextflow.processor.TaskProcessor - [48/cfc788] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD133_knockout_1) Jun-04 22:09:03.585 [Actor Thread 35] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:03.585 [Actor Thread 35] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:03.590 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:03.591 [Task submitter] INFO nextflow.Session - [c0/626fa8] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_1) Jun-04 22:09:03.600 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [13/4c4996] Cached process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (WT_1) Jun-04 22:09:06.040 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 110; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/96/ba62fec3707199d2a215a6c1742111] Jun-04 22:09:06.040 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=120; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Jun-04 22:09:06.047 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:06.047 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:06.047 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:06.048 [Task submitter] INFO nextflow.Session - [6d/1dec7f] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_1) Jun-04 22:09:06.055 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:06.055 [Task submitter] INFO nextflow.Session - [84/7c7cdb] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_1) Jun-04 22:09:06.344 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/80/6610e22b8a247ffd8bc770de8ef317] Jun-04 22:09:06.349 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:06.349 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:06.349 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:06.351 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:06.351 [Task submitter] INFO nextflow.Session - [3d/f0baef] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD133_knockout_2) Jun-04 22:09:10.881 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/3d/f0baefe6877832e5cf67b20e6d3e94] Jun-04 22:09:10.887 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:10.887 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:10.887 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:10.889 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:10.889 [Task submitter] INFO nextflow.Session - [e3/2d2969] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD133_knockout_2) Jun-04 22:09:42.896 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/e3/2d2969d287bc69e1479af0b758f8dd] Jun-04 22:09:42.901 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:42.903 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:42.904 [Task submitter] INFO nextflow.Session - [f1/921709] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (WT_2) Jun-04 22:09:48.418 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 105; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/f1/921709e31d1d3b9f5c1642630235c4] Jun-04 22:09:48.423 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:09:48.423 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:09:48.423 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:09:48.425 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:09:48.425 [Task submitter] INFO nextflow.Session - [5b/c06f4a] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_2) Jun-04 22:10:40.161 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 106; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/5b/c06f4aacc622c76843b58b6c4c35e4] Jun-04 22:10:40.167 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:10:40.169 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:10:40.170 [Task submitter] INFO nextflow.Session - [66/74aaab] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (WT_2) Jun-04 22:10:57.327 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 104; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/66/74aaabf6659aad680dd1b67f661341] Jun-04 22:10:57.331 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:10:57.331 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:10:57.331 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:10:57.333 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:10:57.333 [Task submitter] INFO nextflow.Session - [a4/d6a7f9] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_knockout_1) Jun-04 22:13:52.518 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below ~> TaskHandler[id: 84; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4b/1530e5d3347f85e5893dbed6c1f9d2] ~> TaskHandler[id: 85; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/69/8e979bb27aad0f0e1dbb87da6bc7d6] ~> TaskHandler[id: 115; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/c0/626fa8ec96e6061ff71ae1314d6bf7] ~> TaskHandler[id: 118; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6d/1dec7f71d1b832ba9ec245c222376b] ~> TaskHandler[id: 120; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/84/7c7cdb93ab044fd4e20cc83eb8759b] ~> TaskHandler[id: 116; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/a4/d6a7f94f1f88dd6e7594cd2ae976f2] Jun-04 22:14:04.411 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 8 -- tasks to be submitted are shown below ~> TaskHandler[id: 119; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD133_knockout_1); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/eb/63f99dde250bb84b18163ed7447b65] ~> TaskHandler[id: 121; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_1); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/c9/f402b01465e53b03bd2b19f15d3da1] ~> TaskHandler[id: 122; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_1); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/89/bac12931832d375d540dd09159e447] ~> TaskHandler[id: 123; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_1); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/de/11e52ad1b277a4963000488cac0b59] ~> TaskHandler[id: 124; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD133_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6c/094a2b6ff52bb1142e56641f08064b] ~> TaskHandler[id: 125; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD133_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/bd/df7ad7fa60e639c0af1182764f10ac] ~> TaskHandler[id: 126; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (WT_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/5f/dcc9a7b4d406b3fde1d036ef1c56e6] ~> TaskHandler[id: 127; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (WT_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/72/85edc28cd1e450b82d58068d9c7b00] Jun-04 22:15:21.546 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 116; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/a4/d6a7f94f1f88dd6e7594cd2ae976f2] Jun-04 22:15:21.600 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:15:21.601 [Task submitter] INFO nextflow.Session - [eb/63f99d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD133_knockout_1) Jun-04 22:18:05.715 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/4b/1530e5d3347f85e5893dbed6c1f9d2] Jun-04 22:18:05.723 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_knockout_2)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/4b/1530e5d3347f85e5893dbed6c1f9d2/SNORD97_knockout_2.sortedByCoord.out.bam` (pattern: `SNORD97_knockout_2.sortedByCoord.out.bam`) Jun-04 22:18:05.724 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_knockout_2)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/4b/1530e5d3347f85e5893dbed6c1f9d2/SNORD97_knockout_2.Aligned.sortedByCoord.out.bam` (pattern: `SNORD97_knockout_2.Aligned.sortedByCoord.out.bam`) Jun-04 22:18:05.724 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:18:05.732 [Task submitter] INFO nextflow.Session - [c9/f402b0] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_1) Jun-04 22:18:05.734 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-04 22:18:05.734 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-04 22:18:05.735 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-04 22:18:05.736 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-04 22:18:05.736 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-04 22:18:05.736 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-04 22:18:05.736 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-04 22:18:05.736 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-04 22:18:05.736 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-04 22:18:05.742 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:18:05.742 [Task submitter] INFO nextflow.Session - [89/bac129] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_1) Jun-04 22:18:05.750 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:18:05.751 [Task submitter] INFO nextflow.Session - [6c/094a2b] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD133_knockout_2) Jun-04 22:18:05.778 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:18:05.778 [Task submitter] INFO nextflow.Session - [bd/df7ad7] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD133_knockout_2) Jun-04 22:18:08.215 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 124; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/6c/094a2b6ff52bb1142e56641f08064b] Jun-04 22:18:08.220 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:18:08.220 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:18:08.223 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:18:08.224 [Task submitter] INFO nextflow.Session - [5f/dcc9a7] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (WT_2) Jun-04 22:18:09.296 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 125; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/bd/df7ad7fa60e639c0af1182764f10ac] Jun-04 22:18:09.300 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:18:09.300 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:18:09.307 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:18:09.307 [Task submitter] INFO nextflow.Session - [72/85edc2] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (WT_2) Jun-04 22:18:09.334 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:18:09.335 [Task submitter] INFO nextflow.Session - [4e/1441f6] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_2) Jun-04 22:18:10.321 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 126; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/5f/dcc9a7b4d406b3fde1d036ef1c56e6] Jun-04 22:18:10.326 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:18:10.326 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:18:14.106 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 127; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/72/85edc28cd1e450b82d58068d9c7b00] Jun-04 22:18:14.110 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:18:14.110 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:18:15.113 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:18:15.113 [Task submitter] INFO nextflow.Session - [4a/4a7f07] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_2) Jun-04 22:18:52.533 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 9 -- submitted tasks are shown below ~> TaskHandler[id: 85; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/69/8e979bb27aad0f0e1dbb87da6bc7d6] ~> TaskHandler[id: 115; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/c0/626fa8ec96e6061ff71ae1314d6bf7] ~> TaskHandler[id: 118; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6d/1dec7f71d1b832ba9ec245c222376b] ~> TaskHandler[id: 120; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/84/7c7cdb93ab044fd4e20cc83eb8759b] ~> TaskHandler[id: 119; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD133_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/eb/63f99dde250bb84b18163ed7447b65] ~> TaskHandler[id: 121; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/c9/f402b01465e53b03bd2b19f15d3da1] ~> TaskHandler[id: 122; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/89/bac12931832d375d540dd09159e447] ~> TaskHandler[id: 132; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4e/1441f6d4a9059b44944216738ee619] ~> TaskHandler[id: 135; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4a/4a7f07a6acad2f8c0ee2b3d9a533dd] Jun-04 22:19:05.133 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 7 -- tasks to be submitted are shown below ~> TaskHandler[id: 123; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_1); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/de/11e52ad1b277a4963000488cac0b59] ~> TaskHandler[id: 128; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_1); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/09/6948472d8ed66f9a422c11e17ac815] ~> TaskHandler[id: 130; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD97_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/10/a4b58615d8dff5c5577ff6f3506cf1] ~> TaskHandler[id: 131; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/9c/5951fadb86ace4a2abe3f32b1b0151] ~> TaskHandler[id: 129; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/81/464acea2a78694d3d4acce0fddd1de] ~> TaskHandler[id: 133; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD133_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/02/c58cd6bd61e55a60d060ca73959411] ~> TaskHandler[id: 134; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (WT_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/63/c6c555edf212b6987ad64787dfb130] Jun-04 22:20:29.097 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 119; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD133_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/eb/63f99dde250bb84b18163ed7447b65] Jun-04 22:20:29.106 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:20:29.107 [Task submitter] INFO nextflow.Session - [de/11e52a] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_1) Jun-04 22:21:22.206 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 115; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/c0/626fa8ec96e6061ff71ae1314d6bf7] Jun-04 22:21:22.226 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:21:52.171 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 118; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/6d/1dec7f71d1b832ba9ec245c222376b] Jun-04 22:21:52.190 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:23:36.115 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/69/8e979bb27aad0f0e1dbb87da6bc7d6] Jun-04 22:23:36.127 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:23:36.127 [Task submitter] INFO nextflow.Session - [09/694847] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_1) Jun-04 22:23:36.128 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_133_double_knockout_2)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/69/8e979bb27aad0f0e1dbb87da6bc7d6/SNORD97_133_double_knockout_2.sortedByCoord.out.bam` (pattern: `SNORD97_133_double_knockout_2.sortedByCoord.out.bam`) Jun-04 22:23:36.129 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN (SNORD97_133_double_knockout_2)` is unable to find [UnixPath]: `/data/project/ding_lab/riboseq/work/69/8e979bb27aad0f0e1dbb87da6bc7d6/SNORD97_133_double_knockout_2.Aligned.sortedByCoord.out.bam` (pattern: `SNORD97_133_double_knockout_2.Aligned.sortedByCoord.out.bam`) Jun-04 22:23:36.135 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:23:36.135 [Task submitter] INFO nextflow.Session - [10/a4b586] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD97_knockout_2) Jun-04 22:23:36.138 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Jun-04 22:23:36.138 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Jun-04 22:23:36.138 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<8:1> Jun-04 22:23:36.138 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<9:1> Jun-04 22:23:36.139 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<12:1> Jun-04 22:23:36.139 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<13:1> Jun-04 22:23:36.139 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<14:1> Jun-04 22:23:36.139 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<15:1> Jun-04 22:23:36.139 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN > Skipping output binding because one or more optional files are missing: fileoutparam<16:1> Jun-04 22:23:38.994 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 130; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/10/a4b58615d8dff5c5577ff6f3506cf1] Jun-04 22:23:38.999 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:23:38.999 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:23:38.999 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:23:39.000 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:23:39.000 [Task submitter] INFO nextflow.Session - [9c/5951fa] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_knockout_2) Jun-04 22:23:40.008 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:23:40.008 [Task submitter] INFO nextflow.Session - [0b/609a32] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD97_knockout_2) Jun-04 22:23:41.084 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 140; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/0b/609a32a942dab4588da3ff535cf89e] Jun-04 22:23:41.088 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:23:41.088 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:23:52.593 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 8 -- submitted tasks are shown below ~> TaskHandler[id: 120; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/84/7c7cdb93ab044fd4e20cc83eb8759b] ~> TaskHandler[id: 121; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/c9/f402b01465e53b03bd2b19f15d3da1] ~> TaskHandler[id: 122; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/89/bac12931832d375d540dd09159e447] ~> TaskHandler[id: 132; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4e/1441f6d4a9059b44944216738ee619] ~> TaskHandler[id: 135; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4a/4a7f07a6acad2f8c0ee2b3d9a533dd] ~> TaskHandler[id: 123; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/de/11e52ad1b277a4963000488cac0b59] ~> TaskHandler[id: 128; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/09/6948472d8ed66f9a422c11e17ac815] ~> TaskHandler[id: 131; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/9c/5951fadb86ace4a2abe3f32b1b0151] Jun-04 22:24:06.089 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 7 -- tasks to be submitted are shown below ~> TaskHandler[id: 129; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/81/464acea2a78694d3d4acce0fddd1de] ~> TaskHandler[id: 133; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD133_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/02/c58cd6bd61e55a60d060ca73959411] ~> TaskHandler[id: 134; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (WT_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/63/c6c555edf212b6987ad64787dfb130] ~> TaskHandler[id: 136; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_1); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/27/c909ec2db781f98aa15b2e3789b045] ~> TaskHandler[id: 137; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/73/82c4fe75d7f68d612a36444a13d2e0] ~> TaskHandler[id: 139; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/b5/f869a23b0517e93478b987071f2c85] ~> TaskHandler[id: 138; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_133_double_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/ee/ea2d8d074cca091cffa32828e3fb8c] Jun-04 22:24:10.512 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 131; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/9c/5951fadb86ace4a2abe3f32b1b0151] Jun-04 22:24:10.516 [TaskFinalizer-10] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:24:10.518 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:24:10.518 [Task submitter] INFO nextflow.Session - [81/464ace] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_knockout_2) Jun-04 22:24:18.226 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 129; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/81/464acea2a78694d3d4acce0fddd1de] Jun-04 22:24:18.231 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:24:18.231 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:24:18.231 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:24:18.232 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:24:18.233 [Task submitter] INFO nextflow.Session - [02/c58cd6] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD133_knockout_2) Jun-04 22:24:19.242 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:24:19.242 [Task submitter] INFO nextflow.Session - [7f/660981] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD97_knockout_2) Jun-04 22:24:21.863 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 141; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/7f/66098165017703d16c0ea80365c98f] Jun-04 22:24:21.867 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:24:21.867 [TaskFinalizer-2] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:24:22.869 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:24:22.870 [Task submitter] INFO nextflow.Session - [97/ad8fa2] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_2) Jun-04 22:25:21.651 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 123; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/de/11e52ad1b277a4963000488cac0b59] Jun-04 22:25:21.656 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:25:21.657 [Task submitter] INFO nextflow.Session - [63/c6c555] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (WT_2) Jun-04 22:25:42.580 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 120; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/84/7c7cdb93ab044fd4e20cc83eb8759b] Jun-04 22:25:42.595 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:28:32.988 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 122; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/89/bac12931832d375d540dd09159e447] Jun-04 22:28:33.024 [TaskFinalizer-5] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:28:33.078 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:28:33.108 [Task submitter] INFO nextflow.Session - [27/c909ec] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_1) Jun-04 22:28:52.602 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 8 -- submitted tasks are shown below ~> TaskHandler[id: 121; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/c9/f402b01465e53b03bd2b19f15d3da1] ~> TaskHandler[id: 132; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4e/1441f6d4a9059b44944216738ee619] ~> TaskHandler[id: 135; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4a/4a7f07a6acad2f8c0ee2b3d9a533dd] ~> TaskHandler[id: 128; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/09/6948472d8ed66f9a422c11e17ac815] ~> TaskHandler[id: 133; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD133_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/02/c58cd6bd61e55a60d060ca73959411] ~> TaskHandler[id: 142; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/97/ad8fa2be3daa7bbcef87bf01fa0dad] ~> TaskHandler[id: 134; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/63/c6c555edf212b6987ad64787dfb130] ~> TaskHandler[id: 136; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/27/c909ec2db781f98aa15b2e3789b045] Jun-04 22:29:06.120 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 5 -- tasks to be submitted are shown below ~> TaskHandler[id: 137; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/73/82c4fe75d7f68d612a36444a13d2e0] ~> TaskHandler[id: 139; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/b5/f869a23b0517e93478b987071f2c85] ~> TaskHandler[id: 138; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_133_double_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/ee/ea2d8d074cca091cffa32828e3fb8c] ~> TaskHandler[id: 143; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/43/c0318e60c7f0ecf44b40bd2c7a3435] ~> TaskHandler[id: 144; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_1); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/7a/55305c0449efcaa32af5c5630ce225] Jun-04 22:30:13.564 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 133; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/02/c58cd6bd61e55a60d060ca73959411] Jun-04 22:30:13.608 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:30:13.608 [Task submitter] INFO nextflow.Session - [73/82c4fe] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_2) Jun-04 22:30:29.013 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 137; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/73/82c4fe75d7f68d612a36444a13d2e0] Jun-04 22:30:29.046 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:30:29.046 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:30:29.046 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:30:29.047 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:30:29.048 [Task submitter] INFO nextflow.Session - [b5/f869a2] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_2) Jun-04 22:30:31.357 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 139; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/b5/f869a23b0517e93478b987071f2c85] Jun-04 22:30:31.361 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:30:31.361 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:30:31.361 [TaskFinalizer-8] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT > Skipping output binding because one or more optional files are missing: fileoutparam<3:1> Jun-04 22:30:31.363 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:30:31.365 [Task submitter] INFO nextflow.Session - [ee/ea2d8d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_133_double_knockout_2) Jun-04 22:31:01.219 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 138; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/ee/ea2d8d074cca091cffa32828e3fb8c] Jun-04 22:31:01.223 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:31:01.224 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:31:01.234 [Task submitter] INFO nextflow.Session - [43/c0318e] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_knockout_2) Jun-04 22:31:01.385 [Actor Thread 15] WARN nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /data/project/ding_lab/riboseq/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location Jun-04 22:31:01.385 [Actor Thread 15] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/python:3.10.4 [cache /data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-python-3.10.4.img] Jun-04 22:31:04.395 [Actor Thread 15] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/python:3.10.4 path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-python-3.10.4.img Jun-04 22:33:13.394 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 128; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/09/6948472d8ed66f9a422c11e17ac815] Jun-04 22:33:13.402 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:33:13.402 [Task submitter] INFO nextflow.Session - [7a/55305c] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_1) Jun-04 22:33:17.794 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 121; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/c9/f402b01465e53b03bd2b19f15d3da1] Jun-04 22:33:17.803 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:33:17.804 [Task submitter] INFO nextflow.Session - [fa/aa4233] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_2) Jun-04 22:33:52.620 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 8 -- submitted tasks are shown below ~> TaskHandler[id: 132; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4e/1441f6d4a9059b44944216738ee619] ~> TaskHandler[id: 135; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4a/4a7f07a6acad2f8c0ee2b3d9a533dd] ~> TaskHandler[id: 142; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/97/ad8fa2be3daa7bbcef87bf01fa0dad] ~> TaskHandler[id: 134; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/63/c6c555edf212b6987ad64787dfb130] ~> TaskHandler[id: 136; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/27/c909ec2db781f98aa15b2e3789b045] ~> TaskHandler[id: 143; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/43/c0318e60c7f0ecf44b40bd2c7a3435] ~> TaskHandler[id: 144; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/7a/55305c0449efcaa32af5c5630ce225] ~> TaskHandler[id: 145; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/fa/aa4233bb5e94aba8f1513153c56c72] Jun-04 22:34:06.810 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 3 -- tasks to be submitted are shown below ~> TaskHandler[id: 146; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD97_133_double_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/8f/e56a27ef148af8e6e455d9fc274ac5] ~> TaskHandler[id: 147; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD97_133_double_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/8d/029b4e0a097055553bec61500dbdf6] ~> TaskHandler[id: 148; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE (null); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/96/bbb3f2938a677ee07b5a51663facf8] Jun-04 22:34:26.727 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 134; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/63/c6c555edf212b6987ad64787dfb130] Jun-04 22:34:26.732 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:26.733 [Task submitter] INFO nextflow.Session - [8f/e56a27] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD97_133_double_knockout_2) Jun-04 22:34:26.791 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:26.791 [Task submitter] INFO nextflow.Session - [8d/029b4e] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD97_133_double_knockout_2) Jun-04 22:34:26.812 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:26.813 [Task submitter] INFO nextflow.Session - [96/bbb3f2] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE (null) Jun-04 22:34:27.728 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 147; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/8d/029b4e0a097055553bec61500dbdf6] Jun-04 22:34:27.733 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:34:27.733 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:34:28.734 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:28.735 [Task submitter] INFO nextflow.Session - [b1/4d582f] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_2) Jun-04 22:34:28.739 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:28.739 [Task submitter] INFO nextflow.Session - [24/e72e1e] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD133_knockout_2) Jun-04 22:34:28.745 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:28.745 [Task submitter] INFO nextflow.Session - [dd/38e44d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_133_double_knockout_2) Jun-04 22:34:29.408 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 167; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/dd/38e44d755e42d06ee51be81c637bf5] Jun-04 22:34:29.412 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:29.430 [Task submitter] INFO nextflow.Session - [0f/5f69c7] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_2) Jun-04 22:34:29.923 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 169; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/24/e72e1e2111873da137fea5295418a9] Jun-04 22:34:29.930 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:29.930 [Task submitter] INFO nextflow.Session - [ca/7c293c] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_knockout_2) Jun-04 22:34:30.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 163; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/0f/5f69c7f022110983ce5bc52381ba10] Jun-04 22:34:30.076 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:30.076 [Task submitter] INFO nextflow.Session - [68/63ea39] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD133_knockout_2) Jun-04 22:34:30.505 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 170; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/b1/4d582f0c4d79e6a04c0d60076db4b0] Jun-04 22:34:30.509 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:30.510 [Task submitter] INFO nextflow.Session - [d0/98bcba] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_133_double_knockout_2) Jun-04 22:34:30.956 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 172; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/ca/7c293c2b20199e9ab5a55008de62d3] Jun-04 22:34:30.971 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:30.972 [Task submitter] INFO nextflow.Session - [3b/66f859] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_knockout_2) Jun-04 22:34:31.317 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 146; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/8f/e56a27ef148af8e6e455d9fc274ac5] Jun-04 22:34:31.321 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Jun-04 22:34:31.321 [TaskFinalizer-9] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<2:1> Jun-04 22:34:31.322 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:31.336 [Task submitter] INFO nextflow.Session - [d2/8beea5] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_2) Jun-04 22:34:31.347 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:31.347 [Task submitter] INFO nextflow.Session - [91/b575b2] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_133_double_knockout_2) Jun-04 22:34:31.619 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 165; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/3b/66f8591a0455fc21b5ef22edf28029] Jun-04 22:34:31.623 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:31.623 [Task submitter] INFO nextflow.Session - [4e/3bec5a] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_knockout_2) Jun-04 22:34:32.129 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 173; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/91/b575b2e875e92e65b9bb8f89e7977b] Jun-04 22:34:32.139 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:32.139 [Task submitter] INFO nextflow.Session - [13/f8051a] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD133_knockout_2) Jun-04 22:34:32.348 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 164; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/68/63ea39f989d99c69ecf381cf455611] Jun-04 22:34:32.352 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:32.352 [Task submitter] INFO nextflow.Session - [33/93bc13] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_knockout_1) Jun-04 22:34:32.375 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 171; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/d0/98bcba3e3a4c2b9f4ec6e1c3a210a4] Jun-04 22:34:32.379 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:32.380 [Task submitter] INFO nextflow.Session - [f4/3cd54a] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_133_double_knockout_1) Jun-04 22:34:32.816 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 162; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/13/f8051a9c03240715e5f3d6597a766d] Jun-04 22:34:32.820 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:32.820 [Task submitter] INFO nextflow.Session - [63/eb7627] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_knockout_1) Jun-04 22:34:33.138 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 153; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/33/93bc1305199dad2faf65422caa84a7] Jun-04 22:34:33.143 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:33.143 [Task submitter] INFO nextflow.Session - [15/abba69] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_133_double_knockout_1) Jun-04 22:34:33.163 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 150; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/f4/3cd54a504c9300e2ed7faa5dcf1adc] Jun-04 22:34:33.167 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:33.167 [Task submitter] INFO nextflow.Session - [45/8dd3cb] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD133_knockout_1) Jun-04 22:34:33.684 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 154; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/63/eb7627626553d9c4990c42724fd027] Jun-04 22:34:33.688 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:33.688 [Task submitter] INFO nextflow.Session - [ac/caa934] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_133_double_knockout_1) Jun-04 22:34:34.045 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 151; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/15/abba692941f2d3016464531e1fec88] Jun-04 22:34:34.049 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:34.049 [Task submitter] INFO nextflow.Session - [0a/2990a6] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD133_knockout_1) Jun-04 22:34:34.073 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 168; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/4e/3bec5a7e0a17d976dba6c804712723] Jun-04 22:34:34.077 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:34.077 [Task submitter] INFO nextflow.Session - [0e/45f8b3] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_1) Jun-04 22:34:35.147 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 161; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD133_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/0a/2990a61d05da53bbda6d5ca446aba3] Jun-04 22:34:35.171 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:35.171 [Task submitter] INFO nextflow.Session - [23/848581] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_knockout_1) Jun-04 22:34:35.539 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 152; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/ac/caa9348bee764230c52b8770412cf7] Jun-04 22:34:35.552 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:35.552 [Task submitter] INFO nextflow.Session - [1a/0ab511] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_1) Jun-04 22:34:35.822 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 157; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/0e/45f8b365a7d274e806e014dd12c9ec] Jun-04 22:34:35.827 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:35.828 [Task submitter] INFO nextflow.Session - [ba/d8c3ad] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_1) Jun-04 22:34:36.141 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 156; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/1a/0ab5114b8e39726599629d3764457a] Jun-04 22:34:36.146 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:36.146 [Task submitter] INFO nextflow.Session - [42/d56826] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD133_knockout_1) Jun-04 22:34:36.163 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 160; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD133_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/45/8dd3cbb90ee37ca4f21329f6c0a928] Jun-04 22:34:36.168 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:36.168 [Task submitter] INFO nextflow.Session - [f4/e74bce] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_2) Jun-04 22:34:36.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 166; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/d2/8beea5bd3ec14d1c158a7ee8c29f91] Jun-04 22:34:36.407 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:36.408 [Task submitter] INFO nextflow.Session - [f1/032ed9] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_2) Jun-04 22:34:36.573 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 158; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/ba/d8c3adf7fa9477707f290bc36ad92b] Jun-04 22:34:36.590 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:36.590 [Task submitter] INFO nextflow.Session - [15/1572ad] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_knockout_1) Jun-04 22:34:36.795 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 159; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD133_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/42/d56826ad858a37d3316db66d1edf56] Jun-04 22:34:36.800 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:36.800 [Task submitter] INFO nextflow.Session - [d4/4e4575] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_1) Jun-04 22:34:36.802 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 155; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/23/84858177ba82caea7442809db1534d] Jun-04 22:34:36.807 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:36.807 [Task submitter] INFO nextflow.Session - [cf/45a115] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_133_double_knockout_1) Jun-04 22:34:37.008 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 190; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/f1/032ed9cfac52c1b17cfff4457c34c1] Jun-04 22:34:37.013 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:37.013 [Task submitter] INFO nextflow.Session - [e7/271870] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_knockout_1) Jun-04 22:34:37.251 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 176; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/15/1572ad8ba497ecff4aa0ae03e6b2ed] Jun-04 22:34:37.255 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:37.255 [Task submitter] INFO nextflow.Session - [71/1f294d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_1) Jun-04 22:34:37.700 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 179; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/71/1f294d727c8c902510c1fd347c5a96] Jun-04 22:34:37.705 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:37.706 [Task submitter] INFO nextflow.Session - [d6/8dc58d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_1) Jun-04 22:34:39.459 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 180; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/d6/8dc58db49c4fbe9770ab00e8289fa2] Jun-04 22:34:39.491 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:39.491 [Task submitter] INFO nextflow.Session - [5a/15ace5] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD133_knockout_1) Jun-04 22:34:39.555 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 177; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/e7/271870c2e8fd4aab5beb183ed9be9a] Jun-04 22:34:39.560 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:39.560 [Task submitter] INFO nextflow.Session - [fd/da27be] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_2) Jun-04 22:34:39.816 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 182; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD133_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/5a/15ace541ec0eafcf77fdaca166c14a] Jun-04 22:34:39.822 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:39.823 [Task submitter] INFO nextflow.Session - [35/3fb05d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_2) Jun-04 22:34:41.227 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 188; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/cf/45a11513eda63b90c6a6b12045e7a3] Jun-04 22:34:41.235 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:41.235 [Task submitter] INFO nextflow.Session - [b7/8dab2f] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_133_double_knockout_1) Jun-04 22:34:41.655 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 185; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/b7/8dab2f90e93df085f882a75ad0ea67] Jun-04 22:34:41.662 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:41.662 [Task submitter] INFO nextflow.Session - [d1/2df034] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_133_double_knockout_1) Jun-04 22:34:41.663 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 181; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/d4/4e457599d02813065bf80378b67822] Jun-04 22:34:41.668 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:41.669 [Task submitter] INFO nextflow.Session - [18/6905d6] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD133_knockout_2) Jun-04 22:34:44.125 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 192; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/35/3fb05da0ea36d2ef7585b76b1dc97e] Jun-04 22:34:44.131 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:44.131 [Task submitter] INFO nextflow.Session - [6d/aecb1d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_knockout_2) Jun-04 22:34:44.154 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 186; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/d1/2df034f0fdac0bba3760721347e17a] Jun-04 22:34:44.162 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:44.162 [Task submitter] INFO nextflow.Session - [54/0b25eb] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_knockout_1) Jun-04 22:34:44.523 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 193; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/6d/aecb1d7295ab0a9910a62fdf7cb747] Jun-04 22:34:44.529 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:44.529 [Task submitter] INFO nextflow.Session - [97/12e9ee] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_133_double_knockout_2) Jun-04 22:34:45.289 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 178; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/54/0b25eba2efb7c0cac70eaf08a6e5a3] Jun-04 22:34:45.294 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:45.294 [Task submitter] INFO nextflow.Session - [99/790404] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD133_knockout_1) Jun-04 22:34:46.515 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 191; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/18/6905d6cf58296fdfdea18c03410655] Jun-04 22:34:46.521 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:46.521 [Task submitter] INFO nextflow.Session - [31/9a578d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD133_knockout_2) Jun-04 22:34:46.853 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 187; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/31/9a578df3222d5fce3748bbe33376e2] Jun-04 22:34:46.858 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:46.859 [Task submitter] INFO nextflow.Session - [4a/c4050a] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD133_knockout_2) Jun-04 22:34:48.502 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 189; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/4a/c4050a87214cb83b706f2fb349600d] Jun-04 22:34:48.508 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:48.508 [Task submitter] INFO nextflow.Session - [e5/b66e2d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD133_knockout_1) Jun-04 22:34:50.084 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 183; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD133_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/e5/b66e2d1419fa28deaa230f563d5856] Jun-04 22:34:50.090 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:50.090 [Task submitter] INFO nextflow.Session - [6b/c100d9] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_133_double_knockout_2) Jun-04 22:34:50.315 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 184; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD133_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/99/790404891244c4f59a8ca0c7e8a153] Jun-04 22:34:50.320 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:50.321 [Task submitter] INFO nextflow.Session - [d7/ebd7b6] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_133_double_knockout_2) Jun-04 22:34:50.719 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 196; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/d7/ebd7b6e191ccf2eb15dfb30a345624] Jun-04 22:34:50.724 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:50.725 [Task submitter] INFO nextflow.Session - [4f/be7d97] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_knockout_2) Jun-04 22:34:51.896 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 199; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/97/12e9eec4e51fc7561e3259e761b1a7] Jun-04 22:34:51.902 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:34:51.903 [Task submitter] INFO nextflow.Session - [b0/a24d4b] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_knockout_2) Jun-04 22:34:52.723 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 194; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/fd/da27bebc25b0c15c832ff0eef28dbb] Jun-04 22:34:53.850 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 198; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/6b/c100d9861ecbd0ff18b3a22617aebf] Jun-04 22:34:54.720 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 195; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/b0/a24d4b5dcd94c13d4d5c4d9ed659bf] Jun-04 22:34:56.962 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 197; name: NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/4f/be7d97248c41f6f2558e234b873f32] Jun-04 22:35:46.115 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 132; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/4e/1441f6d4a9059b44944216738ee619] Jun-04 22:35:46.126 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:35:49.618 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 148; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE (null); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/96/bbb3f2938a677ee07b5a51663facf8] Jun-04 22:35:49.651 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:35:49.651 [Task submitter] INFO nextflow.Session - [36/159a68] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_2) Jun-04 22:35:49.673 [Actor Thread 8] WARN nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /data/project/ding_lab/riboseq/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location Jun-04 22:35:49.674 [Actor Thread 8] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/bioconductor-tximeta%3A1.20.1--r43hdfd78af_0 [cache /data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-bioconductor-tximeta%3A1.20.1--r43hdfd78af_0.img] Jun-04 22:36:52.715 [Actor Thread 8] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/bioconductor-tximeta%3A1.20.1--r43hdfd78af_0 path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-bioconductor-tximeta%3A1.20.1--r43hdfd78af_0.img Jun-04 22:38:52.665 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 8 -- submitted tasks are shown below ~> TaskHandler[id: 135; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4a/4a7f07a6acad2f8c0ee2b3d9a533dd] ~> TaskHandler[id: 142; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/97/ad8fa2be3daa7bbcef87bf01fa0dad] ~> TaskHandler[id: 136; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/27/c909ec2db781f98aa15b2e3789b045] ~> TaskHandler[id: 143; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/43/c0318e60c7f0ecf44b40bd2c7a3435] ~> TaskHandler[id: 144; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/7a/55305c0449efcaa32af5c5630ce225] ~> TaskHandler[id: 145; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/fa/aa4233bb5e94aba8f1513153c56c72] ~> TaskHandler[id: 174; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/f4/e74bce71d97f16d1a30f8a2826f599] ~> TaskHandler[id: 149; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/36/159a689f75953b501254ab989624ca] Jun-04 22:39:07.679 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 2 -- tasks to be submitted are shown below ~> TaskHandler[id: 175; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_2); status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/d8/54bb6c67aca1153a08a95fe3e257ab] ~> TaskHandler[id: 200; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT; status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/ef/2f3f088737d9dd021c91a8af04b45a] Jun-04 22:40:27.376 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 136; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/27/c909ec2db781f98aa15b2e3789b045] Jun-04 22:40:27.420 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:40:27.420 [Task submitter] INFO nextflow.Session - [d8/54bb6c] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_2) Jun-04 22:43:52.731 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 8 -- submitted tasks are shown below ~> TaskHandler[id: 135; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4a/4a7f07a6acad2f8c0ee2b3d9a533dd] ~> TaskHandler[id: 142; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/97/ad8fa2be3daa7bbcef87bf01fa0dad] ~> TaskHandler[id: 143; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/43/c0318e60c7f0ecf44b40bd2c7a3435] ~> TaskHandler[id: 144; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_1); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/7a/55305c0449efcaa32af5c5630ce225] ~> TaskHandler[id: 145; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/fa/aa4233bb5e94aba8f1513153c56c72] ~> TaskHandler[id: 174; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/f4/e74bce71d97f16d1a30f8a2826f599] ~> TaskHandler[id: 149; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/36/159a689f75953b501254ab989624ca] ~> TaskHandler[id: 175; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/d8/54bb6c67aca1153a08a95fe3e257ab] Jun-04 22:43:59.620 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 142; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/97/ad8fa2be3daa7bbcef87bf01fa0dad] Jun-04 22:43:59.633 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:44:08.622 [Task submitter] DEBUG n.processor.TaskPollingMonitor - %% executor local > tasks in the submission queue: 1 -- tasks to be submitted are shown below ~> TaskHandler[id: 200; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT; status: NEW; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/ef/2f3f088737d9dd021c91a8af04b45a] Jun-04 22:44:59.566 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 143; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/43/c0318e60c7f0ecf44b40bd2c7a3435] Jun-04 22:44:59.635 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:44:59.635 [Task submitter] INFO nextflow.Session - [ef/2f3f08] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT Jun-04 22:45:33.802 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 200; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT; status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/ef/2f3f088737d9dd021c91a8af04b45a] Jun-04 22:45:33.808 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:45:33.808 [Task submitter] INFO nextflow.Session - [63/b33093] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_2) Jun-04 22:45:33.937 [Actor Thread 39] WARN nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /data/project/ding_lab/riboseq/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location Jun-04 22:45:33.937 [Actor Thread 39] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0 [cache /data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-bioconductor-summarizedexperiment-1.32.0--r43hdfd78af_0.img] Jun-04 22:45:56.154 [Actor Thread 39] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0 path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-bioconductor-summarizedexperiment-1.32.0--r43hdfd78af_0.img Jun-04 22:46:32.834 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 144; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/7a/55305c0449efcaa32af5c5630ce225] Jun-04 22:46:32.853 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:46:32.853 [Task submitter] INFO nextflow.Session - [91/d3096e] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (all_samples) Jun-04 22:47:46.334 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 145; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD133_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/fa/aa4233bb5e94aba8f1513153c56c72] Jun-04 22:47:46.357 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:47:46.357 [Task submitter] INFO nextflow.Session - [67/18ffaf] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (all_samples) Jun-04 22:48:00.704 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 205; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (all_samples); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/91/d3096eb559ee31594e4fcd89a2c911] Jun-04 22:48:00.718 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:48:00.718 [Task submitter] INFO nextflow.Session - [52/011efb] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (all_samples) Jun-04 22:48:13.064 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 203; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (all_samples); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/67/18ffaf34170e68b05c489b82be89e8] Jun-04 22:48:13.070 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:48:13.070 [Task submitter] INFO nextflow.Session - [be/dc9925] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE (all_samples) Jun-04 22:48:26.988 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 202; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (all_samples); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/52/011efb786cbd783b13b762225e6677] Jun-04 22:48:39.784 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 204; name: NFCORE_RIBOSEQ:RIBOSEQ:QUANTIFY_STAR_SALMON:SE_GENE (all_samples); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/be/dc9925e9ef38b686f8d65c7f658c4c] Jun-04 22:48:52.793 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 5 -- submitted tasks are shown below ~> TaskHandler[id: 135; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/4a/4a7f07a6acad2f8c0ee2b3d9a533dd] ~> TaskHandler[id: 174; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/f4/e74bce71d97f16d1a30f8a2826f599] ~> TaskHandler[id: 149; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/36/159a689f75953b501254ab989624ca] ~> TaskHandler[id: 175; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/d8/54bb6c67aca1153a08a95fe3e257ab] ~> TaskHandler[id: 201; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/63/b330932122af29c2722ce16a2a4050] Jun-04 22:49:52.019 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 175; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_QUALITY_RIBOSEQ (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/d8/54bb6c67aca1153a08a95fe3e257ab] Jun-04 22:49:52.039 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:49:52.039 [Task submitter] INFO nextflow.Session - [06/b64f1f] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_2) Jun-04 22:49:52.047 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-04 22:49:52.061 [Task submitter] INFO nextflow.Session - [6a/5cb0ad] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples) Jun-04 22:51:38.156 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 135; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/4a/4a7f07a6acad2f8c0ee2b3d9a533dd] Jun-04 22:51:38.167 [TaskFinalizer-6] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:53:04.801 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 174; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/f4/e74bce71d97f16d1a30f8a2826f599] Jun-04 22:53:04.811 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_RIBOSEQ:RIBOSEQ:RIBOTRICER_DETECTORFS > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Jun-04 22:53:52.834 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 4 -- submitted tasks are shown below ~> TaskHandler[id: 149; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/36/159a689f75953b501254ab989624ca] ~> TaskHandler[id: 201; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/63/b330932122af29c2722ce16a2a4050] ~> TaskHandler[id: 206; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/06/b64f1f58eed7bcfa6338986c115307] ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 22:56:34.284 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 149; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (WT_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/36/159a689f75953b501254ab989624ca] Jun-04 22:58:52.869 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below ~> TaskHandler[id: 201; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/63/b330932122af29c2722ce16a2a4050] ~> TaskHandler[id: 206; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/06/b64f1f58eed7bcfa6338986c115307] ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:03:52.949 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 3 -- submitted tasks are shown below ~> TaskHandler[id: 201; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/63/b330932122af29c2722ce16a2a4050] ~> TaskHandler[id: 206; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_2); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/06/b64f1f58eed7bcfa6338986c115307] ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:07:04.782 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 201; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/63/b330932122af29c2722ce16a2a4050] Jun-04 23:08:29.425 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 206; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_INDIVIDUAL (SNORD97_133_double_knockout_2); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/06/b64f1f58eed7bcfa6338986c115307] Jun-04 23:08:53.040 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:13:53.126 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:18:53.209 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:23:53.289 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:28:53.376 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:33:53.452 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:38:53.529 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:43:53.606 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:48:53.678 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:53:53.749 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-04 23:58:53.834 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-05 00:03:53.913 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-05 00:08:53.987 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-05 00:13:54.069 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: RUNNING; exit: -; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-05 00:15:21.888 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 207; name: NFCORE_RIBOSEQ:RIBOSEQ:RIBOTISH_PREDICT_ALL (allsamples); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/6a/5cb0adcb8f34795dd909d7465a83dd] Jun-05 00:15:21.902 [Actor Thread 47] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 28; slices: 1; internal sort time: 0.004 s; external sort time: 0.002 s; total time: 0.006 s Jun-05 00:15:21.925 [Actor Thread 47] DEBUG nextflow.file.FileCollector - >> temp file exists? false Jun-05 00:15:21.926 [Actor Thread 47] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /data/project/ding_lab/riboseq/work/collect-file/fa2f264194627f479e8215d1b659308d Jun-05 00:15:21.931 [Actor Thread 47] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /data/project/ding_lab/riboseq/work/collect-file/fa2f264194627f479e8215d1b659308d Jun-05 00:15:21.932 [Actor Thread 47] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /scratch/local/nxf-8672363931473032209 Jun-05 00:15:22.070 [Actor Thread 47] WARN nextflow.container.SingularityCache - Singularity cache directory has not been defined -- Remote image will be stored in the path: /data/project/ding_lab/riboseq/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location Jun-05 00:15:22.070 [Actor Thread 47] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0 [cache /data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-multiqc-1.27--pyhdfd78af_0.img] Jun-05 00:15:36.931 [Actor Thread 47] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0 path=/data/project/ding_lab/riboseq/work/singularity/depot.galaxyproject.org-singularity-multiqc-1.27--pyhdfd78af_0.img Jun-05 00:15:36.935 [Actor Thread 46] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/mbansal/.nextflow/assets/nf-core/riboseq/assets/multiqc_config.yml Jun-05 00:15:36.982 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run Jun-05 00:15:36.982 [Task submitter] INFO nextflow.Session - [f5/f7385d] Submitted process > NFCORE_RIBOSEQ:RIBOSEQ:MULTIQC (1) Jun-05 00:15:55.970 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 208; name: NFCORE_RIBOSEQ:RIBOSEQ:MULTIQC (1); status: COMPLETED; exit: 0; error: -; workDir: /data/project/ding_lab/riboseq/work/f5/f7385d88d9172ad2630e3fbbfcc08f] Jun-05 00:15:55.998 [main] DEBUG nextflow.Session - Session await > all processes finished Jun-05 00:15:56.071 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop Jun-05 00:15:56.071 [main] DEBUG nextflow.Session - Session await > all barriers passed Jun-05 00:15:56.074 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false) Jun-05 00:15:56.074 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Jun-05 00:15:56.107 [main] INFO nextflow.Nextflow - -[nf-core/riboseq] Pipeline completed successfully- Jun-05 00:15:56.124 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=102; failedCount=0; ignoredCount=0; cachedCount=106; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=1d 10h 8m 40s; failedDuration=0ms; cachedDuration=3d 20h 4m 15s;loadCpus=0; loadMemory=0; peakRunning=13; peakCpus=33; peakMemory=198 GB; ] Jun-05 00:15:56.124 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Jun-05 00:15:56.157 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Jun-05 00:15:56.727 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Jun-05 00:15:56.998 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Jun-05 00:15:57.067 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-schema@2.3.0' Jun-05 00:15:57.067 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-schema Jun-05 00:15:57.068 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Jun-05 00:15:57.069 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye