Oct-09 09:31:50.842 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: ProxyConfig[protocol=http; host=klone-dip1; port=3128] Oct-09 09:31:50.901 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/denovotranscript -c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config --input /gscratch/scrubbed/strigg/analyses/20240925/samplesheet/samplesheet_test.csv --outdir /gscratch/scrubbed/strigg/analyses/20241009_denovo '--extra_fastp_args=--trim_front1 10 --trim_front2 10' --remove_ribo_rna --assemblers rnaspades --busco_lineage= mollusca_odb10 -resume -with-report nf_report.html -with-trace -with-timeline nf_timeline.html Oct-09 09:31:51.037 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.4 Oct-09 09:31:51.071 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/mmfs1/home/strigg/.nextflow/plugins; core-plugins: nf-amazon@2.5.3,nf-azure@1.6.1,nf-cloudcache@0.4.1,nf-codecommit@0.2.1,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2-patch1,nf-tower@1.9.1,nf-wave@1.4.2-patch1 Oct-09 09:31:51.083 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Oct-09 09:31:51.084 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Oct-09 09:31:51.086 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Oct-09 09:31:51.123 [main] INFO org.pf4j.AbstractPluginManager - No plugins Oct-09 09:31:51.133 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /mmfs1/home/strigg/.nextflow/scm Oct-09 09:31:52.837 [main] DEBUG nextflow.scm.AssetManager - Git config: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/denovotranscript.git Oct-09 09:31:52.883 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Oct-09 09:31:52.908 [main] DEBUG nextflow.scm.AssetManager - Git config: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/denovotranscript.git Oct-09 09:31:53.982 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/nextflow.config Oct-09 09:31:54.000 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /gscratch/srlab/strigg/bin/uw_hyak_srlab.config Oct-09 09:31:54.001 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/nextflow.config Oct-09 09:31:54.001 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /gscratch/srlab/strigg/bin/uw_hyak_srlab.config Oct-09 09:31:54.006 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /mmfs1/home/strigg/.nextflow/secrets/store.json Oct-09 09:31:54.008 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@1320e68a] - activable => nextflow.secret.LocalSecretsProvider@1320e68a Oct-09 09:31:54.032 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` Oct-09 09:31:56.273 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` Oct-09 09:31:56.454 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration Oct-09 09:31:56.455 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/denovotranscript` [lonely_cantor] DSL2 - revision: 27bb1e7924 [master] Oct-09 09:31:56.457 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation@1.1.3] Oct-09 09:31:56.458 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Oct-09 09:31:56.458 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation@1.1.3] Oct-09 09:31:56.458 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3 Oct-09 09:31:56.478 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved Oct-09 09:31:56.478 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3' Oct-09 09:31:56.483 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3 Oct-09 09:31:56.740 [main] DEBUG nextflow.Session - Session UUID: 5ba6b00c-907a-42d8-a460-c42e3f250bd1 Oct-09 09:31:56.740 [main] DEBUG nextflow.Session - Run name: lonely_cantor Oct-09 09:31:56.740 [main] DEBUG nextflow.Session - Executor pool size: 2 Oct-09 09:31:56.746 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Oct-09 09:31:56.752 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Oct-09 09:31:56.779 [main] DEBUG nextflow.cli.CmdRun - Version: 24.04.4 build 5917 Created: 01-08-2024 07:05 UTC (00:05 PDT) System: Linux 4.18.0-513.18.1.el8_9.x86_64 Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.11-internal+0-adhoc..src Encoding: UTF-8 (UTF-8) Process: 69494@n3439 [10.64.66.183] CPUs: 1 - Mem: 100 GB (99.5 GB) - Swap: 1.2 TB (1.2 TB) Oct-09 09:31:56.898 [main] DEBUG nextflow.Session - Work-dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work [gpfs] Oct-09 09:31:56.898 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/bin Oct-09 09:31:56.907 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Oct-09 09:31:56.928 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Oct-09 09:31:57.056 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Oct-09 09:31:57.078 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 2; maxThreads: 1000 Oct-09 09:31:57.458 [main] DEBUG nextflow.Session - Session start Oct-09 09:31:57.460 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /gscratch/scrubbed/strigg/analyses/20241009_denovo/pipeline_info/execution_trace_2024-10-09_09-31-56.txt Oct-09 09:31:57.716 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Oct-09 09:31:59.328 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation Oct-09 09:31:59.336 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation Oct-09 09:31:59.337 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation Oct-09 09:31:59.374 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation Oct-09 09:31:59.375 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation Oct-09 09:31:59.873 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation Oct-09 09:31:59.874 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation Oct-09 09:32:02.641 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation Oct-09 09:32:02.641 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation Oct-09 09:32:02.642 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation Oct-09 09:32:02.644 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation Oct-09 09:32:02.645 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation Oct-09 09:32:03.091 [main] DEBUG nextflow.Nextflow - Using schema file: nextflow_schema.json Oct-09 09:32:03.093 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` Oct-09 09:32:03.102 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/denovotranscript v1.0.0-g27bb1e7 ------------------------------------------------------ Core Nextflow options revision : master runName : lonely_cantor containerEngine : singularity launchDir : /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo workDir : /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work projectDir : /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript userName : strigg profile : standard configFiles :  Input/output options input : /gscratch/scrubbed/strigg/analyses/20240925/samplesheet/samplesheet_test.csv outdir : /gscratch/scrubbed/strigg/analyses/20241009_denovo FastQC/fastp options extra_fastp_args : --trim_front1 10 --trim_front2 10 SortMeRNA options remove_ribo_rna : true Assembly options assemblers : rnaspades BUSCO options busco_lineage :  Institutional config options config_profile_description: UW Hyak Roberts labs cluster profile provided by nf-core/configs. config_profile_contact : Shelly A. Wanamaker @shellywanamaker config_profile_url : https://faculty.washington.edu/sr320/ Max job request options max_cpus : 40 max_memory : 742 GB max_time : 3d !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/denovotranscript for your analysis please cite: * The pipeline * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/denovotranscript/blob/master/CITATIONS.md ------------------------------------------------------ Oct-09 09:32:03.105 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation Oct-09 09:32:03.292 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/gscratch/scrubbed/strigg/analyses/20240925/samplesheet/samplesheet_test.csv' with '/mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/assets/schema_input.json' Oct-09 09:32:03.332 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/gscratch/scrubbed/strigg/analyses/20240925/samplesheet/samplesheet_test.csv' with '/mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/assets/schema_input.json' Oct-09 09:32:03.332 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation Oct-09 09:32:03.334 [main] WARN nextflow.Nextflow - nf-core pipelines do not accept positional arguments. The positional argument `mollusca_odb10` has been detected. HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. Oct-09 09:32:03.348 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: '/gscratch/scrubbed/strigg/analyses/20240925/samplesheet/samplesheet_test.csv' with '/mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/assets/schema_input.json' Oct-09 09:32:03.351 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: '/gscratch/scrubbed/strigg/analyses/20240925/samplesheet/samplesheet_test.csv' with '/mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/assets/schema_input.json' Oct-09 09:32:03.358 [main] WARN n.validation.SamplesheetConverter - Samplesheet warnings: The samplesheet contains following unchecked field(s): [run_accession, experiment_accession, sample_accession, secondary_sample_accession, study_accession, secondary_study_accession, submission_accession, run_alias, experiment_alias, sample_alias, study_alias, library_layout, library_selection, library_source, library_strategy, library_name, instrument_model, instrument_platform, base_count, read_count, tax_id, scientific_name, sample_title, experiment_title, study_title, sample_description, fastq_md5, fastq_bytes, fastq_ftp, fastq_galaxy, fastq_aspera] Oct-09 09:32:03.528 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW Oct-09 09:32:03.535 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*FASTQC_RAW` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW Oct-09 09:32:03.549 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*FASTQC_RAW` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW Oct-09 09:32:03.557 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:03.558 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:03.578 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Oct-09 09:32:03.583 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Oct-09 09:32:03.585 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Oct-09 09:32:03.599 [main] DEBUG n.processor.TaskPollingMonitor - Creating submit rate limit of 1 submissions per 1 seconds Oct-09 09:32:03.625 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Oct-09 09:32:03.716 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP Oct-09 09:32:03.717 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTP` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP Oct-09 09:32:03.739 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:03.739 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:03.772 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM Oct-09 09:32:03.773 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*FASTQC_TRIM` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM Oct-09 09:32:03.774 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*FASTQC_TRIM` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM Oct-09 09:32:03.776 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:03.776 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:03.853 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA Oct-09 09:32:03.853 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SORTMERNA` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA Oct-09 09:32:03.856 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:03.856 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:03.892 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQC_FINAL Oct-09 09:32:03.893 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC_FINAL` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQC_FINAL Oct-09 09:32:03.911 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:03.911 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:03.954 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_FASTQ Oct-09 09:32:03.956 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:03.956 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.007 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES Oct-09 09:32:04.008 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SPADES` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES Oct-09 09:32:04.013 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.013 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.044 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_CAT Oct-09 09:32:04.047 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.047 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.070 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:EVIGENE_TR2AACDS Oct-09 09:32:04.071 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:EVIGENE_TR2AACDS` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:EVIGENE_TR2AACDS Oct-09 09:32:04.073 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.073 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.088 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE Oct-09 09:32:04.089 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:TX2GENE` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE Oct-09 09:32:04.094 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.094 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.125 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO Oct-09 09:32:04.144 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.144 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.181 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST Oct-09 09:32:04.188 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.188 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.217 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE Oct-09 09:32:04.240 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.240 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.267 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_INDEX Oct-09 09:32:04.269 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.270 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.295 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_QUANT Oct-09 09:32:04.300 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.300 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.506 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:MULTIQC Oct-09 09:32:04.508 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:MULTIQC Oct-09 09:32:04.510 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Oct-09 09:32:04.510 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Oct-09 09:32:04.524 [main] DEBUG nextflow.Session - Config process names validation disabled as requested Oct-09 09:32:04.529 [main] DEBUG nextflow.Session - Igniting dataflow network (38) Oct-09 09:32:04.558 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW Oct-09 09:32:04.558 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP Oct-09 09:32:04.558 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM Oct-09 09:32:04.580 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA Oct-09 09:32:04.581 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQC_FINAL Oct-09 09:32:04.596 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_FASTQ Oct-09 09:32:04.611 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES Oct-09 09:32:04.611 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_CAT Oct-09 09:32:04.611 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:EVIGENE_TR2AACDS Oct-09 09:32:04.612 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE Oct-09 09:32:04.612 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO Oct-09 09:32:04.636 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST Oct-09 09:32:04.637 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE Oct-09 09:32:04.637 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_INDEX Oct-09 09:32:04.637 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_QUANT Oct-09 09:32:04.659 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:MULTIQC Oct-09 09:32:04.676 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_d0b8f450f71dfc7a: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/cat/cat/main.nf Script_36a243e2c737dc27: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/local/orp_transrate/main.nf Script_fd62e63acac37503: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/evigene/tr2aacds/main.nf Script_9a9735536805ee91: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../subworkflows/local/utils_nfcore_denovotranscript_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf Script_432e824b8d3b6cf3: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/salmon/quant/main.nf Script_43a0eefac2b1ceca: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/spades/main.nf Script_39c9d2f195f2747c: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/busco/busco/main.nf Script_34a6e65ee7dbdbe0: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../subworkflows/local/utils_nfcore_denovotranscript_pipeline/../../nf-core/utils_nextflow_pipeline/main.nf Script_4d03c228e535e039: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/denovotranscript.nf Script_321cd9384cb1d43b: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../subworkflows/local/utils_nfcore_denovotranscript_pipeline/main.nf Script_a7d371fe23db7aab: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../subworkflows/local/utils_nfcore_denovotranscript_pipeline/../../nf-core/utils_nfvalidation_plugin/main.nf Script_a0f93b4a32030f55: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf Script_15a6f18236447b08: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/cat/fastq/main.nf Script_0900967148a99930: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/sortmerna/main.nf Script_ca3483cfbba7127f: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../subworkflows/nf-core/fastq_trim_fastp_fastqc/../../../modules/nf-core/fastqc/main.nf Script_7bdb792340bdcbe3: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../subworkflows/nf-core/fastq_trim_fastp_fastqc/../../../modules/nf-core/fastp/main.nf Script_9b6b133241201d66: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/trinity/main.nf Script_11299cb12a111d0f: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/multiqc/main.nf Script_cda537213a45fdcd: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/local/rnaquast/main.nf Script_5ccfaa55237746d2: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/gawk/main.nf Script_6e7bd052558e1ef8: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/./workflows/../modules/nf-core/salmon/index/main.nf Script_d909f3e76bc3d3ed: /mmfs1/home/strigg/.nextflow/assets/nf-core/denovotranscript/main.nf Oct-09 09:32:04.677 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Oct-09 09:32:04.677 [main] DEBUG nextflow.Session - Session await Oct-09 09:32:04.789 [Actor Thread 13] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.046 s; total time: 0.047 s Oct-09 09:32:04.790 [Actor Thread 13] DEBUG nextflow.file.FileCollector - >> temp file exists? false Oct-09 09:32:04.790 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/collect-file/cdfc2a36e86090ee4b666d45eb04f020 Oct-09 09:32:04.813 [Actor Thread 3] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.033 s; total time: 0.033 s Oct-09 09:32:04.813 [Actor Thread 3] DEBUG nextflow.file.FileCollector - >> temp file exists? false Oct-09 09:32:04.813 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/collect-file/537d58f944a205fa8d6b780c8f522cb0 Oct-09 09:32:04.830 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/collect-file/537d58f944a205fa8d6b780c8f522cb0 Oct-09 09:32:04.844 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/collect-file/cdfc2a36e86090ee4b666d45eb04f020 Oct-09 09:32:04.857 [Actor Thread 13] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-8381635715395344175 Oct-09 09:32:04.859 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-39461219813416687 Oct-09 09:32:04.957 [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=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img Oct-09 09:32:04.957 [Actor Thread 13] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0; path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-fastp-0.23.4--h5f740d0_0.img Oct-09 09:32:07.111 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (SRX5644304) > jobId: 21274711; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/b3/000963a2aa3130732a049c60dd5676 Oct-09 09:32:07.112 [Task submitter] INFO nextflow.Session - [b3/000963] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (SRX5644304) Oct-09 09:32:07.374 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP (SRX5644304) > jobId: 21274712; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/d8/2d8f0f969aaefeab477e37a74280e7 Oct-09 09:32:07.375 [Task submitter] INFO nextflow.Session - [d8/2d8f0f] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP (SRX5644304) Oct-09 09:33:53.628 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21274712; id: 2; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP (SRX5644304); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/d8/2d8f0f969aaefeab477e37a74280e7 started: 1728491563652; exited: 2024-10-09T16:33:49.020808744Z; ] Oct-09 09:33:53.629 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Oct-09 09:33:53.956 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Oct-09 09:33:53.957 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1> Oct-09 09:33:54.016 [TaskFinalizer-1] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Oct-09 09:33:54.515 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (SRX5644304) > jobId: 21274724; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/91/609118deeb6ea30cf1458ef31c3b7e Oct-09 09:33:54.515 [Task submitter] INFO nextflow.Session - [91/609118] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (SRX5644304) Oct-09 09:33:56.026 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5.8s-database-id98.fasta to work dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/stage-5ba6b00c-907a-42d8-a460-c42e3f250bd1/35/04eb7e93f200af60e0359332112888/rfam-5.8s-database-id98.fasta Oct-09 09:33:56.073 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/rfam-5s-database-id98.fasta to work dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/stage-5ba6b00c-907a-42d8-a460-c42e3f250bd1/ca/34ff3f59f30cd62cf2b2166634b1d5/rfam-5s-database-id98.fasta Oct-09 09:33:56.124 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-arc-16s-id95.fasta to work dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/stage-5ba6b00c-907a-42d8-a460-c42e3f250bd1/f1/987b373ecefd223f7bfda094979be7/silva-arc-16s-id95.fasta Oct-09 09:33:56.157 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-arc-23s-id98.fasta to work dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/stage-5ba6b00c-907a-42d8-a460-c42e3f250bd1/db/76ae22b797c214f734c6bebdb56ea7/silva-arc-23s-id98.fasta Oct-09 09:33:56.197 [FileTransfer-5] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-bac-16s-id90.fasta to work dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/stage-5ba6b00c-907a-42d8-a460-c42e3f250bd1/ed/fa1d4d8ff916cbed45522c21f14a0b/silva-bac-16s-id90.fasta Oct-09 09:33:56.244 [FileTransfer-6] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-bac-23s-id98.fasta to work dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/stage-5ba6b00c-907a-42d8-a460-c42e3f250bd1/ea/8560365958c3a4e219a72e253d957e/silva-bac-23s-id98.fasta Oct-09 09:33:56.294 [FileTransfer-7] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-euk-18s-id95.fasta to work dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/stage-5ba6b00c-907a-42d8-a460-c42e3f250bd1/39/2d96a3a7c132b5b029c4cc5c6f0d9c/silva-euk-18s-id95.fasta Oct-09 09:33:56.323 [FileTransfer-8] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/biocore/sortmerna/v4.3.4/data/rRNA_databases/silva-euk-28s-id98.fasta to work dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/stage-5ba6b00c-907a-42d8-a460-c42e3f250bd1/6a/5b8a346ecb3d9f06f4d90baba70d02/silva-euk-28s-id98.fasta Oct-09 09:33:58.260 [Actor Thread 21] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0; path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-sortmerna-4.3.6--h9ee0642_0.img Oct-09 09:33:58.807 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304) > jobId: 21274725; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 Oct-09 09:33:58.808 [Task submitter] INFO nextflow.Session - [56/cfac33] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304) Oct-09 09:34:23.637 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21274711; id: 1; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (SRX5644304); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/b3/000963a2aa3130732a049c60dd5676 started: 1728491563626; exited: 2024-10-09T16:34:22.191508782Z; ] Oct-09 09:35:53.637 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21274724; id: 3; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM (SRX5644304); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/91/609118deeb6ea30cf1458ef31c3b7e started: 1728491663649; exited: 2024-10-09T16:35:52.319534717Z; ] Oct-09 09:37:08.630 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 09:42:08.640 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 09:47:08.654 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 09:52:08.665 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 09:57:08.672 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 10:02:08.681 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 10:07:08.692 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 10:12:08.699 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 10:17:08.710 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 10:22:08.724 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: -; ] Oct-09 10:24:43.733 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21274725; id: 4; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SORTMERNA (SRX5644304); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/56/cfac331c847e58c4c10ca172917198 started: 1728491663655; exited: 2024-10-09T17:24:38.922618142Z; ] Oct-09 10:24:44.008 [Actor Thread 35] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/ubuntu:20.04; path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-ubuntu-20.04.img Oct-09 10:24:44.239 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQC_FINAL (SRX5644304) > jobId: 21275393; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/b9/40bd956464914cd57a5254649a43d8 Oct-09 10:24:44.239 [Task submitter] INFO nextflow.Session - [b9/40bd95] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQC_FINAL (SRX5644304) Oct-09 10:24:44.406 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_FASTQ (pooled_reads) > jobId: 21275394; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/4b/27da12d4e55da439fb6ccf37151004 Oct-09 10:24:44.406 [Task submitter] INFO nextflow.Session - [4b/27da12] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_FASTQ (pooled_reads) Oct-09 10:27:03.755 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21275393; id: 5; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:FASTQC_FINAL (SRX5644304); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/b9/40bd956464914cd57a5254649a43d8 started: 1728494713736; exited: 2024-10-09T17:27:00.373327485Z; ] Oct-09 10:27:03.788 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21275394; id: 6; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_FASTQ (pooled_reads); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/4b/27da12d4e55da439fb6ccf37151004 started: 1728494818767; exited: 2024-10-09T17:27:01.721954245Z; ] Oct-09 10:27:03.991 [Actor Thread 39] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/spades:4.0.0--h5fb382e_1; path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-spades-4.0.0--h5fb382e_1.img Oct-09 10:27:04.846 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads) > jobId: 21275437; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/09/3cc3ea2ed1896e14e1efff36eb8531 Oct-09 10:27:04.846 [Task submitter] INFO nextflow.Session - [09/3cc3ea] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads) Oct-09 10:27:08.733 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21275437; id: 7; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads); status: SUBMITTED; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/09/3cc3ea2ed1896e14e1efff36eb8531 started: -; exited: -; ] Oct-09 10:32:08.743 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21275437; id: 7; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/09/3cc3ea2ed1896e14e1efff36eb8531 started: 1728494853739; exited: -; ] Oct-09 10:37:08.757 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21275437; id: 7; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/09/3cc3ea2ed1896e14e1efff36eb8531 started: 1728494853739; exited: -; ] Oct-09 10:42:08.765 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21275437; id: 7; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/09/3cc3ea2ed1896e14e1efff36eb8531 started: 1728494853739; exited: -; ] Oct-09 10:45:18.788 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21275437; id: 7; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/09/3cc3ea2ed1896e14e1efff36eb8531 started: 1728494853739; exited: 2024-10-09T17:45:16.813984149Z; ] Oct-09 10:45:18.870 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads)` is unable to find [UnixPath]: `/mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/09/3cc3ea2ed1896e14e1efff36eb8531/warnings.log` (pattern: `warnings.log`) Oct-09 10:45:18.872 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<0:1> Oct-09 10:45:18.872 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Oct-09 10:45:18.890 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<5:1> Oct-09 10:45:18.891 [TaskFinalizer-7] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<7:1> Oct-09 10:45:19.019 [Actor Thread 46] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/pigz:2.3.4 [cache /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-pigz-2.3.4.img] Oct-09 10:45:25.288 [Actor Thread 46] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/pigz:2.3.4 path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-pigz-2.3.4.img Oct-09 10:45:25.546 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_CAT (all_assembled) > jobId: 21276621; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/5d/2adf29893395342ac61c39f7dcc954 Oct-09 10:45:25.546 [Task submitter] INFO nextflow.Session - [5d/2adf29] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_CAT (all_assembled) Oct-09 10:46:38.780 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21276621; id: 8; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:CAT_CAT (all_assembled); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/5d/2adf29893395342ac61c39f7dcc954 started: 1728495998775; exited: 2024-10-09T17:46:36.456328052Z; ] Oct-09 10:46:38.876 [Actor Thread 49] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/evigene:23.7.15--hdfd78af_1 [cache /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-evigene-23.7.15--hdfd78af_1.img] Oct-09 10:47:08.802 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > No more task to compute -- The following nodes are still active: [process] NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:EVIGENE_TR2AACDS status=ACTIVE port 0: (value) bound ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) bound ; channel: program_file port 2: (cntrl) - ; channel: $ [process] NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) bound ; channel: mode port 2: (value) bound ; channel: lineage port 3: (value) bound ; channel: busco_lineages_path port 4: (value) bound ; channel: config_file port 5: (cntrl) - ; channel: $ [process] NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (cntrl) - ; channel: $ [process] NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE status=ACTIVE port 0: (value) OPEN ; channel: - port 1: (value) bound ; channel: - port 2: (value) bound ; channel: reference port 3: (cntrl) - ; channel: $ [process] NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_INDEX status=ACTIVE port 0: (value) OPEN ; channel: transcript_fasta port 1: (cntrl) - ; channel: $ [process] NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_QUANT status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) OPEN ; channel: index port 2: (value) OPEN ; channel: transcript_fasta port 3: (value) bound ; channel: lib_type port 4: (cntrl) - ; channel: $ [process] NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:MULTIQC status=ACTIVE port 0: (value) OPEN ; channel: multiqc_files port 1: (value) bound ; channel: multiqc_config port 2: (value) bound ; channel: extra_multiqc_config port 3: (value) bound ; channel: multiqc_logo port 4: (cntrl) - ; channel: $ Oct-09 10:48:07.907 [Actor Thread 49] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/evigene:23.7.15--hdfd78af_1 path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-evigene-23.7.15--hdfd78af_1.img Oct-09 10:48:08.183 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:EVIGENE_TR2AACDS (all_assembled) > jobId: 21276986; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/c7/2b96452bd557b33327069d72014d7e Oct-09 10:48:08.184 [Task submitter] INFO nextflow.Session - [c7/2b9645] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:EVIGENE_TR2AACDS (all_assembled) Oct-09 10:51:53.835 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21276986; id: 9; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:EVIGENE_TR2AACDS (all_assembled); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/c7/2b96452bd557b33327069d72014d7e started: 1728496108825; exited: 2024-10-09T17:51:52.163119485Z; ] Oct-09 10:51:54.153 [Actor Thread 59] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/rnaquast:2.3.0--h9ee0642_0 [cache /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-rnaquast-2.3.0--h9ee0642_0.img] Oct-09 10:51:54.216 [Actor Thread 62] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/busco:5.7.1--pyhdfd78af_0 [cache /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-busco-5.7.1--pyhdfd78af_0.img] Oct-09 10:51:54.226 [Actor Thread 63] INFO nextflow.container.SingularityCache - Pulling Singularity image docker://docker.io/avanibhojwani/orp_transrate:1.0.3_cv1.2 [cache /gscratch/scrubbed/srlab/.apptainer/docker.io-avanibhojwani-orp_transrate-1.0.3_cv1.2.img] Oct-09 10:51:54.229 [Actor Thread 61] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0 [cache /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-salmon-1.10.1--h7e5ed60_0.img] Oct-09 10:51:54.278 [Actor Thread 65] INFO nextflow.container.SingularityCache - Pulling Singularity image https://depot.galaxyproject.org/singularity/gawk:5.3.0 [cache /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-gawk-5.3.0.img] Oct-09 10:51:58.397 [Actor Thread 65] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/gawk:5.3.0 path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-gawk-5.3.0.img Oct-09 10:51:58.561 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE (all_assembled) > jobId: 21277357; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/d9/9951430a05744f7e97465b1b7384a4 Oct-09 10:51:58.561 [Task submitter] INFO nextflow.Session - [d9/995143] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE (all_assembled) Oct-09 10:52:08.823 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21277357; id: 13; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE (all_assembled); status: SUBMITTED; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/d9/9951430a05744f7e97465b1b7384a4 started: -; exited: -; ] Oct-09 10:52:29.368 [Actor Thread 63] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=docker://docker.io/avanibhojwani/orp_transrate:1.0.3_cv1.2 path=/gscratch/scrubbed/srlab/.apptainer/docker.io-avanibhojwani-orp_transrate-1.0.3_cv1.2.img Oct-09 10:52:29.880 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE (pooled_reads) > jobId: 21277370; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/a0/a1b51a4c0a6f4fdd5935156260f6a3 Oct-09 10:52:29.881 [Task submitter] INFO nextflow.Session - [a0/a1b51a] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE (pooled_reads) Oct-09 10:52:30.826 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21277357; id: 13; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TX2GENE (all_assembled); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/d9/9951430a05744f7e97465b1b7384a4 started: 1728496345829; exited: 2024-10-09T17:52:27.223616742Z; ] Oct-09 10:52:31.852 [Actor Thread 61] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0 path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-salmon-1.10.1--h7e5ed60_0.img Oct-09 10:52:32.028 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_INDEX (all_assembled.okay.mrna) > jobId: 21277373; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/5d/d705e2f90721ff6cd084a02d7d08dd Oct-09 10:52:32.028 [Task submitter] INFO nextflow.Session - [5d/d705e2] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_INDEX (all_assembled.okay.mrna) Oct-09 10:53:50.827 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21277373; id: 14; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_INDEX (all_assembled.okay.mrna); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/5d/d705e2f90721ff6cd084a02d7d08dd started: 1728496405822; exited: 2024-10-09T17:53:47.867606216Z; ] Oct-09 10:53:51.232 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_QUANT (SRX5644304) > jobId: 21277391; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/03/465e0162394d95b15f6c6ecb4cdcf1 Oct-09 10:53:51.232 [Task submitter] INFO nextflow.Session - [03/465e01] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_QUANT (SRX5644304) Oct-09 10:56:40.842 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21277391; id: 15; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SALMON_QUANT (SRX5644304); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/03/465e0162394d95b15f6c6ecb4cdcf1 started: 1728496540824; exited: 2024-10-09T17:56:40.724461519Z; ] Oct-09 10:57:10.822 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21277370; id: 11; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE (pooled_reads); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/a0/a1b51a4c0a6f4fdd5935156260f6a3 started: 1728496380832; exited: -; ] Oct-09 10:57:16.836 [Actor Thread 62] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/busco:5.7.1--pyhdfd78af_0 path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-busco-5.7.1--pyhdfd78af_0.img Oct-09 10:57:18.373 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled) > jobId: 21277442; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/41/f7ae53efafe62ef07f9ec609aee385 Oct-09 10:57:18.373 [Task submitter] INFO nextflow.Session - [41/f7ae53] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled) Oct-09 10:57:19.189 [Actor Thread 59] DEBUG nextflow.container.SingularityCache - Singularity pull complete image=https://depot.galaxyproject.org/singularity/rnaquast:2.3.0--h9ee0642_0 path=/gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-rnaquast-2.3.0--h9ee0642_0.img Oct-09 10:57:20.871 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST (all_assembled) > jobId: 21277443; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/b8/cf00b2309e5f787930e535d1857344 Oct-09 10:57:20.871 [Task submitter] INFO nextflow.Session - [b8/cf00b2] Submitted process > NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST (all_assembled) Oct-09 10:58:15.837 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21277442; id: 10; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled); status: COMPLETED; exit: 2; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/41/f7ae53efafe62ef07f9ec609aee385 started: 1728496680828; exited: 2024-10-09T17:58:13.743278559Z; ] Oct-09 10:58:15.880 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled); work-dir=/mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/41/f7ae53efafe62ef07f9ec609aee385 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)` terminated with an error exit status (2) Oct-09 10:58:16.115 [TaskFinalizer-3] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)' Caused by: Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO (all_assembled)` terminated with an error exit status (2) Command executed: # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute) # Check for container variable initialisation script and source it. if [ -f "/usr/local/env-activate.sh" ]; then set +u # Otherwise, errors out because of various unbound variables . "/usr/local/env-activate.sh" set -u fi # If the augustus config directory is not writable, then copy to writeable area if [ ! -w "${AUGUSTUS_CONFIG_PATH}" ]; then # Create writable tmp directory for augustus AUG_CONF_DIR=$( mktemp -d -p $PWD ) cp -r $AUGUSTUS_CONFIG_PATH/* $AUG_CONF_DIR export AUGUSTUS_CONFIG_PATH=$AUG_CONF_DIR echo "New AUGUSTUS_CONFIG_PATH=${AUGUSTUS_CONFIG_PATH}" fi # Ensure the input is uncompressed INPUT_SEQS=input_seqs mkdir "$INPUT_SEQS" cd "$INPUT_SEQS" for FASTA in ../tmp_input/*; do if [ "${FASTA##*.}" == 'gz' ]; then gzip -cdf "$FASTA" > $( basename "$FASTA" .gz ) else ln -s "$FASTA" . fi done cd .. busco \ --cpu 6 \ --in "$INPUT_SEQS" \ --out all_assembled--busco \ --mode transcriptome \ --lineage_dataset \ \ \ # clean up rm -rf "$INPUT_SEQS" # Move files to avoid staging/publishing issues mv all_assembled--busco/batch_summary.txt all_assembled--busco.batch_summary.txt mv all_assembled--busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found." cat <<-END_VERSIONS > versions.yml "NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:BUSCO_BUSCO": busco: $( busco --version 2>&1 | sed 's/^BUSCO //' ) END_VERSIONS Command exit status: 2 Command output: New AUGUSTUS_CONFIG_PATH=/gscratch/scrubbed/srlab/nxf.OnByylhFGt/tmp.CaFy5VTnmk Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS] busco: error: argument -l/--lineage_dataset: expected one argument Work dir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/41/f7ae53efafe62ef07f9ec609aee385 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` Oct-09 10:58:16.132 [TaskFinalizer-3] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Oct-09 10:58:16.165 [TaskFinalizer-3] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting Oct-09 10:58:16.166 [main] DEBUG nextflow.Session - Session await > all processes finished Oct-09 10:58:16.172 [Actor Thread 48] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 13; slices: 1; internal sort time: 0.003 s; external sort time: 0.001 s; total time: 0.004 s Oct-09 10:58:16.176 [Actor Thread 48] DEBUG nextflow.file.FileCollector - >> temp file exists? false Oct-09 10:58:16.176 [Actor Thread 48] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/collect-file/4908ecde5ea4de362863c39e711b2364 Oct-09 10:58:16.199 [Actor Thread 48] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/collect-file/4908ecde5ea4de362863c39e711b2364 Oct-09 10:58:16.200 [Actor Thread 48] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-13996718040676142633 Oct-09 10:58:16.203 [Actor Thread 55] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:MULTIQC; work-dir=null error [java.lang.IllegalStateException]: Cannot obtain the semaphore to fork operator's body. Oct-09 10:58:21.176 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21277443; id: 12; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST (all_assembled); status: COMPLETED; exit: 1; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/b8/cf00b2309e5f787930e535d1857344 started: 1728496680842; exited: 2024-10-09T17:58:17.436125022Z; ] Oct-09 10:58:21.177 [TaskFinalizer-4] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST (all_assembled); work-dir=/mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/b8/cf00b2309e5f787930e535d1857344 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:RNAQUAST (all_assembled)` terminated with an error exit status (1) Oct-09 11:02:11.174 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below ~> TaskHandler[jobId: 21277370; id: 11; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE (pooled_reads); status: RUNNING; exit: -; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/a0/a1b51a4c0a6f4fdd5935156260f6a3 started: 1728496380832; exited: -; ] Oct-09 11:02:31.185 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 21277370; id: 11; name: NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE (pooled_reads); status: COMPLETED; exit: 0; error: -; workDir: /mmfs1/gscratch/scrubbed/strigg/analyses/20241009_denovo/work/a0/a1b51a4c0a6f4fdd5935156260f6a3 started: 1728496380832; exited: 2024-10-09T18:02:28.467673013Z; ] Oct-09 11:02:31.185 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop Oct-09 11:02:31.186 [main] DEBUG nextflow.Session - Session await > all barriers passed Oct-09 11:02:31.304 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false) Oct-09 11:02:36.308 [main] INFO nextflow.util.ThreadPoolHelper - Waiting for file transfers to complete (1 files) Oct-09 11:02:46.616 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Oct-09 11:02:46.622 [main] INFO nextflow.Nextflow - -[nf-core/denovotranscript] Pipeline completed with errors- Oct-09 11:02:46.627 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=13; failedCount=2; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=16h 32m 19s; failedDuration=3m 32s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=3; peakCpus=24; peakMemory=144 GB; ] Oct-09 11:02:46.627 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Oct-09 11:02:46.656 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Oct-09 11:02:47.409 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Oct-09 11:02:47.973 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Oct-09 11:02:48.098 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-validation@1.1.3' Oct-09 11:02:48.098 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation Oct-09 11:02:48.100 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Oct-09 11:02:48.101 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye