wf-transcriptome crash on fastcat

[Bhersbach]

Operating System

Other Linux (please specify below)

Other Linux

No response

Workflow Version

v1.6.1

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-transcriptomes
--fastq '/localdata/xgv106/fastq/'
--ref_annotation '/home/xgv106/references/Homo_sapiens.GRCh38.113.chr.gtf'
--ref_genome '/home/xgv106/references/Homo_sapiens.GRCh38.dna.primary_assembly.fa'
--sample_sheet '/localdata/xgv106/sample_sheet.csv'
--out_dir /home/xgv106/output/
--igv
--threads 32
--transcriptome_source reference-guided
--cdna_kit SQK-PCB114
-profile standard

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

I have tried running the demo workflow and all works as intended. When I run this on my own data, I get to the stage of fastcat and then the script randomly aborts, but there is no clear reason for it that I could identify. On the attached screenshots you can see the output when it fails. It seems to be independed of sample, it has happened for barcode01 as well as 05 and 06 when I tried debugging.

nextflow.txt

Relevant log output

Jan-08 15:17:34.874 [main] DEBUG nextflow.cli.Launcher - $> nextflow run epi2me-labs/wf-transcriptomes --fastq /localdata/xgv106/fastq/ --ref_annotation /home/xgv106/references/Homo_sapiens.GRCh38.113.chr.gtf --ref_genome /home/xgv106/references/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sample_sheet /localdata/xgv106/sample_sheet.csv --out_dir /home/xgv106/output/ --igv --threads 32 --transcriptome_source reference-guided --cdna_kit SQK-PCB114 -profile standard
Jan-08 15:17:35.041 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 24.10.3
Jan-08 15:17:35.071 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/xgv106/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Jan-08 15:17:35.109 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jan-08 15:17:35.111 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jan-08 15:17:35.115 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jan-08 15:17:35.135 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Jan-08 15:17:35.152 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/xgv106/.nextflow/scm
Jan-08 15:17:36.031 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/.git/config; branch: null; remote: origin; url: https://github.com/epi2me-labs/wf-transcriptomes.git
Jan-08 15:17:36.063 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jan-08 15:17:36.073 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/.git/config; branch: null; remote: origin; url: https://github.com/epi2me-labs/wf-transcriptomes.git
Jan-08 15:17:36.987 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/nextflow.config
Jan-08 15:17:36.991 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/nextflow.config
Jan-08 15:17:37.002 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/xgv106/.nextflow/secrets/store.json
Jan-08 15:17:37.006 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@1e3f0aea] - activable => nextflow.secret.LocalSecretsProvider@1e3f0aea
Jan-08 15:17:37.026 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jan-08 15:17:37.283 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jan-08 15:17:37.285 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/epi2me-labs/wf-transcriptomes` [tender_raman] DSL2 - revision: a33f3b967c [master]
Jan-08 15:17:37.287 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jan-08 15:17:37.288 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jan-08 15:17:37.361 [main] DEBUG nextflow.Session - Session UUID: 086b6afb-161e-4041-bb7b-8b4bc6f174e6
Jan-08 15:17:37.362 [main] DEBUG nextflow.Session - Run name: tender_raman
Jan-08 15:17:37.362 [main] DEBUG nextflow.Session - Executor pool size: 128
Jan-08 15:17:37.374 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jan-08 15:17:37.381 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=384; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jan-08 15:17:37.407 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 24.10.3 build 5933
  Created: 16-12-2024 15:34 UTC (16:34 CEST)
  System: Linux 5.14.0-427.37.1.el9_4.x86_64
  Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.13+11-LTS
  Encoding: UTF-8 (UTF-8)
  Process: [email protected] [10.84.10.0]
  CPUs: 128 - Mem: 995 GB (65.4 GB) - Swap: 10 GB (10 GB)
Jan-08 15:17:37.442 [main] DEBUG nextflow.Session - Work-dir: /home/xgv106/work [nfs]
Jan-08 15:17:37.494 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jan-08 15:17:37.507 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jan-08 15:17:37.587 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jan-08 15:17:37.601 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 129; maxThreads: 1000
Jan-08 15:17:37.808 [main] DEBUG nextflow.Session - Session start
Jan-08 15:17:37.811 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/xgv106/output/execution/trace.txt
Jan-08 15:17:37.824 [main] DEBUG nextflow.Session - Using default localLib path: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/lib
Jan-08 15:17:37.831 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/lib
Jan-08 15:17:37.832 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/lib/nfcore_external_java_deps.jar
Jan-08 15:17:41.868 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jan-08 15:17:43.908 [main] INFO  nextflow.Nextflow - 
�[0;92m||||||||||   �[0m�[2m_____ ____ ___ ____  __  __ _____      _       _
�[0;92m||||||||||  �[0m�[2m| ____|  _ \_ _|___ \|  \/  | ____|    | | __ _| |__  ___
�[0;33m|||||       �[0m�[2m|  _| | |_) | |  __) | |\/| |  _| _____| |/ _` | '_ \/ __|
�[0;33m|||||       �[0m�[2m| |___|  __/| | / __/| |  | | |__|_____| | (_| | |_) \__ \
�[0;94m||||||||||  �[0m�[2m|_____|_|  |___|_____|_|  |_|_____|    |_|\__,_|_.__/|___/
�[0;94m||||||||||  �[0m�[1mwf-transcriptomes v1.6.1-ga33f3b9�[0m
�[2m--------------------------------------------------------------------------------�[0m
�[1mCore Nextflow options�[0m
  �[0;34mrevision       : �[0;32mmaster�[0m
  �[0;34mrunName        : �[0;32mtender_raman�[0m
  �[0;34mcontainerEngine: �[0;32mdocker�[0m
  �[0;34mcontainer      : �[0;32m[withLabel:isoforms:ontresearch/wf-transcriptomes:shad8671ea3a8ed52f2c0f40355e8eb5c6f00d2cbda, withLabel:wf_common:ontresearch/wf-common:shaabceef445fb63214073cbf5836fdd33c04be4ac7]�[0m
  �[0;34mlaunchDir      : �[0;32m/home/xgv106�[0m
  �[0;34mworkDir        : �[0;32m/home/xgv106/work�[0m
  �[0;34mprojectDir     : �[0;32m/home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes�[0m
  �[0;34muserName       : �[0;32mxgv106�[0m
  �[0;34mprofile        : �[0;32mstandard�[0m
  �[0;34mconfigFiles    : �[0;32m/home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/nextflow.config�[0m

�[1mInput Options�[0m
  �[0;34mfastq          : �[0;32m/localdata/xgv106/fastq/�[0m
  �[0;34mref_genome     : �[0;32m/home/xgv106/references/Homo_sapiens.GRCh38.dna.primary_assembly.fa�[0m
  �[0;34mref_annotation : �[0;32m/home/xgv106/references/Homo_sapiens.GRCh38.113.chr.gtf�[0m

�[1mOutput Options�[0m
  �[0;34mout_dir        : �[0;32m/home/xgv106/output/�[0m
  �[0;34migv            : �[0;32mtrue�[0m

�[1mSample Options�[0m
  �[0;34msample_sheet   : �[0;32m/localdata/xgv106/sample_sheet.csv�[0m

�[1mAdvanced Options�[0m
  �[0;34mthreads        : �[0;32m32�[0m
  �[0;34mcdna_kit       : �[0;32mSQK-PCB114�[0m

!! Only displaying parameters that differ from the pipeline defaults !!
�[2m--------------------------------------------------------------------------------�[0m
If you use epi2me-labs/wf-transcriptomes for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x


�[2m--------------------------------------------------------------------------------�[0m
This is epi2me-labs/wf-transcriptomes v1.6.1-ga33f3b9.
�[2m--------------------------------------------------------------------------------�[0m
Jan-08 15:17:44.132 [main] INFO  nextflow.Nextflow - Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Jan-08 15:17:44.509 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `ingress,wf_common` for process with name validate_sample_sheet
Jan-08 15:17:44.541 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.542 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.546 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jan-08 15:17:44.550 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=128; memory=995 GB; capacity=128; pollInterval=100ms; dumpInterval=5m
Jan-08 15:17:44.552 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Jan-08 15:17:44.683 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `ingress,wf_common` for process with name fastcat
Jan-08 15:17:44.685 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.685 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.704 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:preprocess_ref_annotation
Jan-08 15:17:44.705 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.705 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.709 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:collectFastqIngressResultsInDir
Jan-08 15:17:44.710 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.710 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.715 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:getVersions
Jan-08 15:17:44.716 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.716 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.718 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:getParams
Jan-08 15:17:44.719 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.719 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.742 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:preprocess_reads
Jan-08 15:17:44.744 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.744 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.770 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:build_minimap_index
Jan-08 15:17:44.771 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.771 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.774 [main] INFO  nextflow.Nextflow - Doing reference based transcript analysis
Jan-08 15:17:44.786 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:reference_assembly:map_reads
Jan-08 15:17:44.787 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.787 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.797 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:split_bam
Jan-08 15:17:44.798 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.799 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.812 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:assemble_transcripts
Jan-08 15:17:44.815 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.815 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.831 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:merge_gff_bundles
Jan-08 15:17:44.833 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.833 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.849 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:run_gffcompare
Jan-08 15:17:44.852 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.852 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.889 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name pipeline:get_transcriptome
Jan-08 15:17:44.891 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.891 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.937 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `wf_common` for process with name pipeline:makeReport
Jan-08 15:17:44.940 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.940 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:44.992 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `wf_common` for process with name pipeline:faidx
Jan-08 15:17:44.993 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:44.993 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:45.052 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:wf_common` matches labels `wf_common` for process with name pipeline:configure_igv
Jan-08 15:17:45.053 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:45.054 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:45.071 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:isoforms` matches labels `isoforms` for process with name publish_results
Jan-08 15:17:45.072 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jan-08 15:17:45.072 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jan-08 15:17:45.077 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: preprocess_ref_transcriptome, checkSampleSheetCondition, move_or_compress_fq_file, mergeTPM, pipeline:getParams, pipeline:get_transcriptome, deAnalysis, checkBamHeaders, mergeBams, pipeline:reference_assembly:map_reads, pipeline:split_bam, collectFastqIngressResultsInDir, makeReport, getVersions, assemble_transcripts, get_transcriptome, merge_transcriptomes, validateIndex, preprocess_reads, bamstats, fastcat, plotResults, map_reads, pipeline:configure_igv, samtools_index, getParams, preprocess_ref_annotation, sortBam, merge_gff_bundles, validate_sample_sheet, pipeline:assemble_transcripts, pipeline:makeReport, publish_results, decompress_transcriptome, map_transcriptome, pipeline:merge_gff_bundles, build_minimap_index, run_gffcompare, configure_igv, pipeline:collectFastqIngressResultsInDir, count_transcripts, faidx, pipeline:faidx, pipeline:getVersions, pipeline:preprocess_reads, gz_faidx, pipeline:build_minimap_index, split_fq_file, mergeCounts, decompress_ref, split_bam, check_annotation_strand, build_minimap_index_transcriptome, decompress_annotation, pipeline:run_gffcompare, pipeline:preprocess_ref_annotation, catSortBams
Jan-08 15:17:45.079 [main] DEBUG nextflow.Session - Igniting dataflow network (27)
Jan-08 15:17:45.080 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > validate_sample_sheet
Jan-08 15:17:45.088 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastcat
Jan-08 15:17:45.089 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:preprocess_ref_annotation
Jan-08 15:17:45.090 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:collectFastqIngressResultsInDir
Jan-08 15:17:45.091 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getVersions
Jan-08 15:17:45.092 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getParams
Jan-08 15:17:45.093 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:preprocess_reads
Jan-08 15:17:45.094 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:build_minimap_index
Jan-08 15:17:45.094 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:reference_assembly:map_reads
Jan-08 15:17:45.096 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:split_bam
Jan-08 15:17:45.097 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:assemble_transcripts
Jan-08 15:17:45.098 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:merge_gff_bundles
Jan-08 15:17:45.098 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:run_gffcompare
Jan-08 15:17:45.099 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:get_transcriptome
Jan-08 15:17:45.099 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:makeReport
Jan-08 15:17:45.100 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:faidx
Jan-08 15:17:45.101 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:configure_igv
Jan-08 15:17:45.101 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > publish_results
Jan-08 15:17:45.101 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_3c04764f1da692a5: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/./subworkflows/reference_assembly.nf
  Script_6813fc658b72b7cb: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/./subworkflows/differential_expression.nf
  Script_1582b4c2a4962737: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/./lib/common.nf
  Script_3b6c0bd93b6e0e1b: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/main.nf
  Script_9674c65acf93e4e1: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/./lib/ingress.nf
Jan-08 15:17:45.101 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
Jan-08 15:17:45.102 [main] DEBUG nextflow.Session - Session await
Jan-08 15:17:45.186 [Actor Thread 109] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /home/xgv106/.nextflow/assets/epi2me-labs/wf-transcriptomes/bin/workflow-glue
Jan-08 15:17:45.297 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:45.300 [Task submitter] INFO  nextflow.Session - [f5/df45a4] Submitted process > pipeline:getParams
Jan-08 15:17:45.321 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:45.322 [Task submitter] INFO  nextflow.Session - [e9/c6813e] Submitted process > pipeline:build_minimap_index (1)
Jan-08 15:17:45.339 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:45.340 [Task submitter] INFO  nextflow.Session - [ac/ce9076] Submitted process > pipeline:faidx (1)
Jan-08 15:17:45.358 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:45.359 [Task submitter] INFO  nextflow.Session - [54/bed3b2] Submitted process > pipeline:preprocess_ref_annotation
Jan-08 15:17:45.375 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:45.376 [Task submitter] INFO  nextflow.Session - [c0/0c6577] Submitted process > pipeline:getVersions
Jan-08 15:17:45.391 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:45.391 [Task submitter] INFO  nextflow.Session - [37/a0ac2e] Submitted process > validate_sample_sheet
Jan-08 15:17:46.414 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: pipeline:getParams; status: COMPLETED; exit: 0; error: -; workDir: /home/xgv106/work/f5/df45a46338a40ae1fd2481dd34cd3d]
Jan-08 15:17:46.416 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=384; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jan-08 15:17:46.755 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: validate_sample_sheet; status: COMPLETED; exit: 0; error: -; workDir: /home/xgv106/work/37/a0ac2e2c3adf3ddb7cd714b88eb815]
Jan-08 15:17:46.774 [TaskFinalizer-2] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=384; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jan-08 15:17:46.840 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:46.840 [Task submitter] INFO  nextflow.Session - [0b/b8d789] Submitted process > fastcat (1)
Jan-08 15:17:46.857 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:46.857 [Task submitter] INFO  nextflow.Session - [14/89f388] Submitted process > fastcat (2)
Jan-08 15:17:46.873 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:46.874 [Task submitter] INFO  nextflow.Session - [90/4bb92a] Submitted process > fastcat (3)
Jan-08 15:17:46.897 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:46.898 [Task submitter] INFO  nextflow.Session - [ff/3edcd0] Submitted process > fastcat (4)
Jan-08 15:17:46.918 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:46.919 [Task submitter] INFO  nextflow.Session - [69/0075a5] Submitted process > fastcat (5)
Jan-08 15:17:46.936 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:17:46.937 [Task submitter] INFO  nextflow.Session - [81/3c43a0] Submitted process > fastcat (6)
Jan-08 15:17:53.957 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: pipeline:getVersions; status: COMPLETED; exit: 0; error: -; workDir: /home/xgv106/work/c0/0c6577b4205484fda38b730693332a]
Jan-08 15:17:56.425 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: pipeline:preprocess_ref_annotation; status: COMPLETED; exit: 0; error: -; workDir: /home/xgv106/work/54/bed3b2014dfa8c8b59bbcd34ad2c05]
Jan-08 15:17:56.738 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: pipeline:faidx (1); status: COMPLETED; exit: 0; error: -; workDir: /home/xgv106/work/ac/ce90760b64d0291e55f17ac607acd2]
Jan-08 15:19:22.479 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: pipeline:build_minimap_index (1); status: COMPLETED; exit: 0; error: -; workDir: /home/xgv106/work/e9/c6813e3785c9d5a9b4c1b750e3e7d0]
Jan-08 15:22:44.726 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[id: 7; name: fastcat (1); status: RUNNING; exit: -; error: -; workDir: /home/xgv106/work/0b/b8d7898d5678db28eb5a449c7a3a93]
~> TaskHandler[id: 8; name: fastcat (2); status: RUNNING; exit: -; error: -; workDir: /home/xgv106/work/14/89f388b4c1f84fd6d26bf16eb64b8f]
~> TaskHandler[id: 9; name: fastcat (3); status: RUNNING; exit: -; error: -; workDir: /home/xgv106/work/90/4bb92a914f5bed03905a9dcacd180c]
~> TaskHandler[id: 10; name: fastcat (4); status: RUNNING; exit: -; error: -; workDir: /home/xgv106/work/ff/3edcd0980dacb901effe19870fa127]
~> TaskHandler[id: 11; name: fastcat (5); status: RUNNING; exit: -; error: -; workDir: /home/xgv106/work/69/0075a5a5a4047010132f45f6344b5a]
~> TaskHandler[id: 12; name: fastcat (6); status: RUNNING; exit: -; error: -; workDir: /home/xgv106/work/81/3c43a026fc8c14d2f30c5b2623dfe2]
Jan-08 15:26:11.082 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: fastcat (4); status: COMPLETED; exit: 0; error: -; workDir: /home/xgv106/work/ff/3edcd0980dacb901effe19870fa127]
Jan-08 15:26:11.177 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:26:11.178 [Task submitter] INFO  nextflow.Session - [ac/1db887] Submitted process > pipeline:collectFastqIngressResultsInDir (1)
Jan-08 15:26:11.193 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Jan-08 15:26:11.194 [Task submitter] INFO  nextflow.Session - [0b/e04632] Submitted process > pipeline:preprocess_reads (1)
Jan-08 15:26:12.075 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: pipeline:collectFastqIngressResultsInDir (1); status: COMPLETED; exit: 0; error: -; workDir: /home/xgv106/work/ac/1db88779e9c371d915a3e805fc6585]

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[nrhorner]

Hi @Bhersbach

Sorry that you're having issues with the workflow.
Is it possible you were running multiple workflow instances from the dame directory? These warnings indicate there was.

Workflow runs must be set off in their own directory.

[Bhersbach]

Thanks for the reply @nrhorner! Turned out the folder where the work directory was placed ran out space, which caused the issue. After changing this the workflow ran without any problems!

If I could maybe ask another question, as I am new to Oxford Nanopore sequencing. I have been reading through #63 and think I understood from this that, to detect potentially novel isoforms, other tools need to be used. Is this correct? In short, we are looking to determine the different transcript isoforms of our gene of interest, which may include isoform that have not yet been annotated. Would the tools mentioned in #63 indeed by the right option here?