sarahjeeeze
commented
3 months ago Hi, your annotation file might be ok. Can you successfully run the example data set in the readme? Just want to check its not an environment error.
Closed aaannaw closed 3 weeks ago
sarahjeeeze
commented
3 months ago Hi, your annotation file might be ok. Can you successfully run the example data set in the readme? Just want to check its not an environment error.
sarahjeeeze
commented
3 weeks ago Closing a no response since March
Rpowellnz
commented
3 weeks ago Hi there,
I've encountered the same error - I'd had some trouble with nextflow, but managed to run the test data successfully just before attempting these analyses. The error message and nextflow log are pasted below. Any suggestions would be greatly appreciated!
ERROR ~ Error executing process > 'pipeline:preprocess_ref_annotation'
Caused by:
Process pipeline:preprocess_ref_annotation terminated for an unknown reason -- Likely it has been terminated by the external system
Command executed:
sed -i -e 's/transcript_id "";//g' Homo_sapiens.GRCh38.111.gtf mv Homo_sapiens.GRCh38.111.gtf "amended.Homo_sapiens.GRCh38.111.gtf"
Command output: (empty)
Work dir: /tmp/powry48p-wf-transcriptomes-work/69/c443b5618eea2371a2a4b96862a09a
Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line
-- Check '.nextflow.log' file for details
[powry48p@aoraki01 ~]$ more .nextflow.log
Jun-07 08:59:47.763 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -w /tmp/powry48p-wf-transcriptomes-work/ epi2me-labs/wf-transcriptomes --fastq /home/powry48p/Desktop/202404ONT/Barcodes/ --de_analysis --ref_genome /home/powry48p/Desktop/202404ONT/reference/ref_genome/Homo_sapiens.GRCh38.dna_rm.primary_assembly.fa --transcriptome-source reference-guided --ref_annotation
/home/powry48p/Desktop/202404ONT/reference/ref_annotation/Homo_sapiens.GRCh38.111.gtf --direct_rna --minimap2_index_opts '-k 15' --sample_sheet /home/powry48p/Desktop/202404ONT/sample_sheet.
csv --jaffal_refBase /home/powry48p/Desktop/202404ONT/JAFFA_REFERENCE_FILES_HG38_GENCODE22.V2 --jaffal_genome hg38.fa --jaffal_annotation genCode22 -profile singularity --out_dir /projects/h
ealth_sciences/oms/pathology/powry48p/202404slam-lung-full
Jun-07 08:59:47.847 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1
Jun-07 08:59:47.862 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/powry48p/.nextflow/plugins; core-plugins: nf-amazon@
2.1.4,nf-azure@1.3.3,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.1
Jun-07 08:59:47.871 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-07 08:59:47.872 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-07 08:59:47.874 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jun-07 08:59:47.883 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jun-07 08:59:47.894 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/powry48p/.nextflow/scm
Jun-07 08:59:48.471 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/.git/config; branch: master; remote: origin; url: https
://github.com/epi2me-labs/wf-transcriptomes.git
Jun-07 08:59:48.485 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Jun-07 08:59:48.492 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/.git/config; branch: master; remote: origin; url: https
://github.com/epi2me-labs/wf-transcriptomes.git
Jun-07 08:59:49.623 [main] INFO nextflow.scm.AssetManager - NOTE: Your local project version looks outdated - a different revision is available in the remote repository [9353e23cc9]
Jun-07 08:59:49.629 [main] DEBUG nextflow.config.ConfigBuilder - Found config home: /home/powry48p/.nextflow/config
Jun-07 08:59:49.629 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/nextflow.config
Jun-07 08:59:49.630 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/powry48p/.nextflow/config
Jun-07 08:59:49.630 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/nextflow.config
Jun-07 08:59:49.637 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: singularity
Jun-07 08:59:49.658 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: singularity
Jun-07 08:59:49.753 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, conda, singularity, awsbatch, local]
Jun-07 08:59:49.775 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Jun-07 08:59:49.775 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/epi2me-labs/wf-transcriptomes [intergalactic_lichterman] DSL2 - revision: 999fb4e44a [master]
Jun-07 08:59:49.776 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-07 08:59:49.776 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-07 08:59:49.778 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/powry48p/.nextflow/secrets/store.json
Jun-07 08:59:49.780 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@40943a6] - activable => nextflow.secret.LocalSecretsProvi
der@40943a6
Jun-07 08:59:49.821 [main] DEBUG nextflow.Session - Session UUID: 6fdda031-1fe6-44fe-a2be-332eed3c4b13
Jun-07 08:59:49.821 [main] DEBUG nextflow.Session - Run name: intergalactic_lichterman
Jun-07 08:59:49.822 [main] DEBUG nextflow.Session - Executor pool size: 32
Jun-07 08:59:49.828 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-07 08:59:49.830 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=fa
lse
Jun-07 08:59:49.850 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.10.1 build 5891
Created: 12-01-2024 22:01 UTC (13-01-2024 11:01 NZDT)
System: Linux 5.14.0-284.18.1.el9_2.x86_64
Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 17.0.11+9
Encoding: UTF-8 (UTF-8)
Process: 1544890@aoraki01 [192.168.55.161]
CPUs: 32 - Mem: 125.4 GB (99.4 GB) - Swap: 0 (0)
Jun-07 08:59:49.867 [main] DEBUG nextflow.Session - Work-dir: /tmp/powry48p-wf-transcriptomes-work [xfs]
Jun-07 08:59:49.879 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-07 08:59:49.886 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-07 08:59:49.930 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-07 08:59:49.937 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Jun-07 08:59:50.008 [main] DEBUG nextflow.Session - Session start
Jun-07 08:59:50.011 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /projects/health_sciences/oms/pathology/powry48p/202404slam-lung-full/execution/trace.txt
Jun-07 08:59:50.018 [main] DEBUG nextflow.Session - Using default localLib path: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/lib
Jun-07 08:59:50.021 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/lib
Jun-07 08:59:50.021 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/lib/nfcore_external_java_deps.jar
Jun-07 08:59:51.603 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-07 08:59:52.203 [main] WARN nextflow.Nextflow - Found unexpected parameters:
Core Nextflow options revision : master runName : intergalactic_lichterman containerEngine : singularity container : [withLabel:isoforms:ontresearch/wf-transcriptomes:shae7c9f184996a384e99be68e790f0612f0c732867, withLabel:wf_common:ontresearch/wf-common:sha1c5febff9f75143 710826498b093d9769a5edbb9] launchDir : /home/powry48p workDir : /tmp/powry48p-wf-transcriptomes-work projectDir : /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes userName : powry48p profile : singularity configFiles : /home/powry48p/.nextflow/config, /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/nextflow.config
Input Options fastq : /home/powry48p/Desktop/202404ONT/Barcodes/ ref_genome : /home/powry48p/Desktop/202404ONT/reference/ref_genome/Homo_sapiens.GRCh38.dna_rm.primary_assembly.fa ref_annotation : /home/powry48p/Desktop/202404ONT/reference/ref_annotation/Homo_sapiens.GRCh38.111.gtf direct_rna : true
Output Options out_dir : /projects/health_sciences/oms/pathology/powry48p/202404slam-lung-full
Sample Options sample_sheet : /home/powry48p/Desktop/202404ONT/sample_sheet.csv
Options for reference-based workflow minimap2_index_opts: -k 15
Gene Fusion Detection Options jaffal_refBase : /home/powry48p/Desktop/202404ONT/JAFFA_REFERENCE_FILES_HG38_GENCODE22.V2 jaffal_genome : hg38.fa
Differential Expression Options de_analysis : true
If you use epi2me-labs/wf-transcriptomes for your analysis please cite:
Jun-07 08:59:53.441 [main] INFO nextflow.Nextflow - Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Jun-07 08:59:53.904 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wf_common matches labels ingress,wf_common for process with name validate_sample_sheet
Jun-07 08:59:53.915 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:53.915 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:53.922 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm
Jun-07 08:59:53.925 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m
Jun-07 08:59:53.926 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm)
Jun-07 08:59:53.928 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m
Jun-07 08:59:54.035 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:wf_common matches labels ingress,wf_common for process with name fastcat
Jun-07 08:59:54.036 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.037 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.046 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:preprocess_ref_annotation
Jun-07 08:59:54.046 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.046 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.050 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:collectFastqIngressResultsInDir
Jun-07 08:59:54.050 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.050 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:getVersions
Jun-07 08:59:54.053 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.053 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.055 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:getParams
Jun-07 08:59:54.055 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.056 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.069 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:build_minimap_index
Jun-07 08:59:54.070 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.070 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.071 [main] INFO nextflow.Nextflow - Doing reference based transcript analysis
Jun-07 08:59:54.081 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:reference_assembly:map_reads
Jun-07 08:59:54.082 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.082 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.090 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:split_bam
Jun-07 08:59:54.090 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.090 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.093 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:assemble_transcripts
Jun-07 08:59:54.094 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.094 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.098 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:merge_gff_bundles
Jun-07 08:59:54.098 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.098 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.101 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:run_gffcompare
Jun-07 08:59:54.102 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.102 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.109 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:get_transcriptome
Jun-07 08:59:54.110 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.110 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.114 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:gene_fusions:jaffal
Jun-07 08:59:54.115 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.115 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.127 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:merge_transcriptomes
Jun-07 08:59:54.127 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.127 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.130 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:differential_expression:checkSa
mpleSheetCondition
Jun-07 08:59:54.130 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.130 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.135 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:differential_expression:build_m
inimap_index_transcriptome
Jun-07 08:59:54.135 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.135 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.138 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:differential_expression:map_tra
nscriptome
Jun-07 08:59:54.138 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.138 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.141 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:differential_expression:count_t
ranscripts
Jun-07 08:59:54.141 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.141 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.142 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:differential_expression:mergeCo
unts
Jun-07 08:59:54.143 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.143 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.144 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:differential_expression:mergeTP
M
Jun-07 08:59:54.144 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.144 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.146 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:differential_expression:deAnaly
sis
Jun-07 08:59:54.146 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.146 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.149 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:differential_expression:plotRes
ults
Jun-07 08:59:54.150 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.150 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.156 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name pipeline:makeReport
Jun-07 08:59:54.156 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.156 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.165 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:isoforms matches labels isoforms for process with name output
Jun-07 08:59:54.165 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm
Jun-07 08:59:54.165 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm'
Jun-07 08:59:54.166 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: preprocess_ref_transcriptome, checkSampleSheetCondition, move_or_compress_fq_file, mergeTPM, pipeline:getPa
rams, pipeline:get_transcriptome, deAnalysis, checkBamHeaders, mergeBams, output, pipeline:reference_assembly:map_reads, pipeline:split_bam, collectFastqIngressResultsInDir, makeReport, getV
ersions, assemble_transcripts, get_transcriptome, merge_transcriptomes, preprocess_reads, pipeline:gene_fusions:jaffal, bamstats, pipeline:differential_expression:count_transcripts, pipeline
:differential_expression:deAnalysis, fastcat, plotResults, pipeline:differential_expression:mergeCounts, map_reads, getParams, preprocess_ref_annotation, sortBam, merge_gff_bundles, validate
_sample_sheet, pipeline:assemble_transcripts, pipeline:differential_expression:plotResults, jaffal, pipeline:makeReport, pipeline:differential_expression:checkSampleSheetCondition, decompres
s_transcriptome, map_transcriptome, pipeline:merge_gff_bundles, pipeline:merge_transcriptomes, build_minimap_index, pipeline:differential_expression:mergeTPM, run_gffcompare, pipeline:collec
tFastqIngressResultsInDir, count_transcripts, pipeline:getVersions, pipeline:build_minimap_index, pipeline:differential_expression:build_minimap_index_transcriptome, mergeCounts, pipeline:di
fferential_expression:map_transcriptome, decompress_ref, split_bam, build_minimap_index_transcriptome, decompress_annotation, pipeline:run_gffcompare, pipeline:preprocess_ref_annotation, cat
SortBams
Jun-07 08:59:54.167 [main] DEBUG nextflow.Session - Igniting dataflow network (29)
Jun-07 08:59:54.167 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > validate_sample_sheet
Jun-07 08:59:54.171 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > fastcat
Jun-07 08:59:54.171 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:preprocess_ref_annotation
Jun-07 08:59:54.171 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:collectFastqIngressResultsInDir
Jun-07 08:59:54.171 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getVersions
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:getParams
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:build_minimap_index
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:reference_assembly:map_reads
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:split_bam
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:assemble_transcripts
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:merge_gff_bundles
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:run_gffcompare
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:get_transcriptome
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:gene_fusions:jaffal
Jun-07 08:59:54.172 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:merge_transcriptomes
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:differential_expression:checkSampleSheetCondition
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:differential_expression:build_minimap_index_transcriptome
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:differential_expression:map_transcriptome
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:differential_expression:count_transcripts
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:differential_expression:mergeCounts
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:differential_expression:mergeTPM
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:differential_expression:deAnalysis
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:differential_expression:plotResults
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pipeline:makeReport
Jun-07 08:59:54.173 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > output
Jun-07 08:59:54.173 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_6c9ad54f8f06decd: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/./subworkflows/reference_assembly.nf
Script_52f11d1ddf9ca2a2: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/./lib/ingress.nf
Script_05eaa6b24b9dd568: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/./subworkflows/JAFFAL/gene_fusions.nf
Script_eb93bcc3448c341a: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/main.nf
Script_b280fdb3f732bae1: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/./subworkflows/differential_expression.nf
Jun-07 08:59:54.173 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jun-07 08:59:54.173 [main] DEBUG nextflow.Session - Session await
Jun-07 08:59:54.204 [Actor Thread 32] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://ontresearch/wf-common:sha1c5febff9f75143710826498b093d9769a
5edbb9; path=/tmp/powry48p-wf-transcriptomes-work/singularity/ontresearch-wf-common-sha1c5febff9f75143710826498b093d9769a5edbb9.img
Jun-07 08:59:54.204 [Actor Thread 31] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://ontresearch/wf-transcriptomes:shae7c9f184996a384e99be68e790
f0612f0c732867; path=/tmp/powry48p-wf-transcriptomes-work/singularity/ontresearch-wf-transcriptomes-shae7c9f184996a384e99be68e790f0612f0c732867.img
Jun-07 08:59:54.218 [Actor Thread 26] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /home/powry48p/.nextflow/assets/epi2me-labs/wf-transcriptomes/bin/workflow-glue
Jun-07 08:59:54.277 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process pipeline:preprocess_ref_annotation > jobId: 489569; workDir: /tmp/powry48p-wf-transcr
iptomes-work/69/c443b5618eea2371a2a4b96862a09a
Jun-07 08:59:54.277 [Task submitter] INFO nextflow.Session - [69/c443b5] Submitted process > pipeline:preprocess_ref_annotation
Jun-07 08:59:54.291 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process pipeline:getParams > jobId: 489570; workDir: /tmp/powry48p-wf-transcriptomes-work/32/
c8608d374dca730e09b594b8019abd
Jun-07 08:59:54.291 [Task submitter] INFO nextflow.Session - [32/c8608d] Submitted process > pipeline:getParams
Jun-07 08:59:54.302 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process pipeline:build_minimap_index (1) > jobId: 489571; workDir: /tmp/powry48p-wf-transcrip
tomes-work/fe/1945dc799d9f172f6b78b157063639
Jun-07 08:59:54.302 [Task submitter] INFO nextflow.Session - [fe/1945dc] Submitted process > pipeline:build_minimap_index (1)
Jun-07 08:59:54.313 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process pipeline:getVersions > jobId: 489572; workDir: /tmp/powry48p-wf-transcriptomes-work/5
e/6506df772e195d53a4b5b3db000b6e
Jun-07 08:59:54.313 [Task submitter] INFO nextflow.Session - [5e/6506df] Submitted process > pipeline:getVersions
Jun-07 08:59:54.325 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process validate_sample_sheet > jobId: 489573; workDir: /tmp/powry48p-wf-transcriptomes-work/
94/bc915a67142cdc607ba4b15072b42f
Jun-07 08:59:54.325 [Task submitter] INFO nextflow.Session - [94/bc915a] Submitted process > validate_sample_sheet
Jun-07 08:59:54.335 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process pipeline:differential_expression:checkSampleSheetCondition > jobId: 489574; workDir:
/tmp/powry48p-wf-transcriptomes-work/44/e480a37028ef62b58ef456a9fcfade
Jun-07 08:59:54.335 [Task submitter] INFO nextflow.Session - [44/e480a3] Submitted process > pipeline:differential_expression:checkSampleSheetCondition
Jun-07 09:02:38.931 [Task monitor] DEBUG nextflow.file.FileHelper - NFS path (false): /tmp/powry48p-wf-transcriptomes-work
Jun-07 09:04:58.933 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 6 -- submitted tasks are shown below
~> TaskHandler[jobId: 489569; id: 1; name: pipeline:preprocess_ref_annotation; status: RUNNING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/69/c443b5618eea2371a2a4b96862
a09a started: 1717707598949; exited: -; ]
~> TaskHandler[jobId: 489570; id: 3; name: pipeline:getParams; status: RUNNING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/32/c8608d374dca730e09b594b8019abd started: 17
17707598950; exited: -; ]
~> TaskHandler[jobId: 489571; id: 5; name: pipeline:build_minimap_index (1); status: RUNNING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/fe/1945dc799d9f172f6b78b1570636
39 started: 1717707598950; exited: -; ]
~> TaskHandler[jobId: 489572; id: 2; name: pipeline:getVersions; status: RUNNING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/5e/6506df772e195d53a4b5b3db000b6e started:
1717707598951; exited: -; ]
~> TaskHandler[jobId: 489573; id: 4; name: validate_sample_sheet; status: RUNNING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/94/bc915a67142cdc607ba4b15072b42f started:
1717707598952; exited: -; ]
~> TaskHandler[jobId: 489574; id: 6; name: pipeline:differential_expression:checkSampleSheetCondition; status: RUNNING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/44/e4
80a37028ef62b58ef456a9fcfade started: 1717707598953; exited: -; ]
Jun-07 09:07:03.938 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 489569; id: 1; name: pipeline:preprocess_ref_annotation;
status: RUNNING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/69/c443b5618eea2371a2a4b96862a09a started: 1717707598949; exited: -; ] -- exitStatusReadTimeoutMillis: 2700
00; delta: 270005
Current queue status:
job: 486434: RUNNING
Content of workDir: /tmp/powry48p-wf-transcriptomes-work/69/c443b5618eea2371a2a4b96862a09a
null
Jun-07 09:07:03.939 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 489569; id: 1; name: pipeline:preprocess_ref_annotation; status: COMPLETED; exit
: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/69/c443b5618eea2371a2a4b96862a09a started: 1717707598949; exited: -; ]
Jun-07 09:07:03.942 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:preprocess_ref_annotation; work-dir=/tmp/powry48p-wf-transcriptomes-work/69/c443b5618eea2371a2a4b96862a09a
error [nextflow.exception.ProcessFailedException]: Process pipeline:preprocess_ref_annotation terminated for an unknown reason -- Likely it has been terminated by the external system
Jun-07 09:07:03.948 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'null' -- Cause: java.nio.file.NoSuchFileException: /tmp/powry48p-wf-transcriptomes-wor
k/69/c443b5618eea2371a2a4b96862a09a/.command.out
Jun-07 09:07:03.948 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'null' -- Cause: java.nio.file.NoSuchFileException: /tmp/powry48p-wf-transcriptomes-work
/69/c443b5618eea2371a2a4b96862a09a/.command.err
Jun-07 09:07:03.948 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'null' -- Cause: java.nio.file.NoSuchFileException: /tmp/powry48p-wf-transcriptomes-work
/69/c443b5618eea2371a2a4b96862a09a/.command.log
Jun-07 09:07:03.949 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'pipeline:preprocess_ref_annotation'
Caused by:
Process pipeline:preprocess_ref_annotation terminated for an unknown reason -- Likely it has been terminated by the external system
Command executed:
sed -i -e 's/transcript_id "";//g' Homo_sapiens.GRCh38.111.gtf mv Homo_sapiens.GRCh38.111.gtf "amended.Homo_sapiens.GRCh38.111.gtf"
Command output: (empty)
Work dir: /tmp/powry48p-wf-transcriptomes-work/69/c443b5618eea2371a2a4b96862a09a
Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line
Jun-07 09:07:03.957 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process pipeline:preprocess_ref_annotation terminated for an unknown reason -- Likely it has been term
inated by the external system
Jun-07 09:07:03.967 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
[process] fastcat
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (value) bound ; channel: extra_args
port 2: (cntrl) - ; channel: $
[process] pipeline:collectFastqIngressResultsInDir status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] pipeline:reference_assembly:map_reads status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] pipeline:split_bam status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] pipeline:assemble_transcripts status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: use_ref_ann port 2: (cntrl) - ; channel: $
[process] pipeline:merge_gff_bundles status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] pipeline:get_transcriptome status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] pipeline:gene_fusions:jaffal status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (value) bound ; channel: refBase port 2: (value) bound ; channel: genome port 3: (value) bound ; channel: annotation port 4: (cntrl) - ; channel: $
[process] pipeline:differential_expression:map_transcriptome status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] pipeline:differential_expression:count_transcripts status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
[process] pipeline:differential_expression:mergeCounts status=ACTIVE port 0: (value) OPEN ; channel: counts port 1: (cntrl) - ; channel: $
[process] pipeline:differential_expression:mergeTPM status=ACTIVE port 0: (value) OPEN ; channel: counts port 1: (cntrl) - ; channel: $
[process] output status=ACTIVE port 0: (queue) OPEN ; channel: - port 1: (cntrl) - ; channel: $
Jun-07 09:07:03.967 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'null' -- Cause: java.nio.file.NoSuchFileException: /tmp/powry48p-wf-transcriptomes-work /69/c443b5618eea2371a2a4b96862a09a/.command.err Jun-07 09:07:03.967 [Task monitor] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'null' -- Cause: java.nio.file.NoSuchFileException: /tmp/powry48p-wf-transcriptomes-wor k/69/c443b5618eea2371a2a4b96862a09a/.command.out Jun-07 09:07:05.180 [main] DEBUG nextflow.Session - Session await > all processes finished Jun-07 09:07:05.181 [main] DEBUG nextflow.Session - Session await > all barriers passed Jun-07 09:07:05.182 [main] DEBUG nextflow.processor.TaskRun - Unable to dump error of process 'null' -- Cause: java.nio.file.NoSuchFileException: /tmp/powry48p-wf-transcriptomes-work/69/c443 b5618eea2371a2a4b96862a09a/.command.err Jun-07 09:07:05.182 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 489570; id: 3; name: pipeline:getParams; status: RUNNING ; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/32/c8608d374dca730e09b594b8019abd started: 1717707598950; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 27124 9 Current queue status:
job: 486434: RUNNING
Content of workDir: /tmp/powry48p-wf-transcriptomes-work/32/c8608d374dca730e09b594b8019abd
null
Jun-07 09:07:05.182 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 489570; id: 3; name: pipeline:getParams; status: COMPLETED; exit: -; error: -; w
orkDir: /tmp/powry48p-wf-transcriptomes-work/32/c8608d374dca730e09b594b8019abd started: 1717707598950; exited: -; ]
Jun-07 09:07:05.182 [main] DEBUG nextflow.processor.TaskRun - Unable to dump output of process 'null' -- Cause: java.nio.file.NoSuchFileException: /tmp/powry48p-wf-transcriptomes-work/69/c44
3b5618eea2371a2a4b96862a09a/.command.out
Jun-07 09:07:05.182 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:getParams; work-dir=/tmp/powry48p-wf-transcriptomes-work/32/c8608d374dca730e09b594b8019abd
error [nextflow.exception.ProcessFailedException]: Process pipeline:getParams terminated for an unknown reason -- Likely it has been terminated by the external system
Jun-07 09:07:05.183 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 489571; id: 5; name: pipeline:build_minimap_index (1); s
tatus: RUNNING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/fe/1945dc799d9f172f6b78b157063639 started: 1717707598950; exited: -; ] -- exitStatusReadTimeoutMillis: 270000
; delta: 271251
Current queue status:
job: 486434: RUNNING
Content of workDir: /tmp/powry48p-wf-transcriptomes-work/fe/1945dc799d9f172f6b78b157063639
null
Jun-07 09:07:05.183 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 489571; id: 5; name: pipeline:build_minimap_index (1); status: COMPLETED; exit:
-; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/fe/1945dc799d9f172f6b78b157063639 started: 1717707598950; exited: -; ]
Jun-07 09:07:05.183 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:build_minimap_index (1); work-dir=/tmp/powry48p-wf-transcriptomes-work/fe/1945dc799d9f172f6b78b157063639
error [nextflow.exception.ProcessFailedException]: Process pipeline:build_minimap_index (1) terminated for an unknown reason -- Likely it has been terminated by the external system
Jun-07 09:07:05.184 [Actor Thread 24] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Jun-07 09:07:05.184 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 489572; id: 2; name: pipeline:getVersions; status: RUNNI
NG; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/5e/6506df772e195d53a4b5b3db000b6e started: 1717707598951; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 271
252
Current queue status:
job: 486434: RUNNING
Content of workDir: /tmp/powry48p-wf-transcriptomes-work/5e/6506df772e195d53a4b5b3db000b6e
null
Jun-07 09:07:05.184 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 489572; id: 2; name: pipeline:getVersions; status: COMPLETED; exit: -; error: -;
workDir: /tmp/powry48p-wf-transcriptomes-work/5e/6506df772e195d53a4b5b3db000b6e started: 1717707598951; exited: -; ]
Jun-07 09:07:05.184 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:getVersions; work-dir=/tmp/powry48p-wf-transcriptomes-work/5e/6506df772e195d53a4b5b3db000b6e
error [nextflow.exception.ProcessFailedException]: Process pipeline:getVersions terminated for an unknown reason -- Likely it has been terminated by the external system
Jun-07 09:07:05.185 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 489573; id: 4; name: validate_sample_sheet; status: RUNN
ING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/94/bc915a67142cdc607ba4b15072b42f started: 1717707598952; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 27
1253
Current queue status:
job: 486434: RUNNING
Content of workDir: /tmp/powry48p-wf-transcriptomes-work/94/bc915a67142cdc607ba4b15072b42f
null
Jun-07 09:07:05.185 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 489573; id: 4; name: validate_sample_sheet; status: COMPLETED; exit: -; error: -
; workDir: /tmp/powry48p-wf-transcriptomes-work/94/bc915a67142cdc607ba4b15072b42f started: 1717707598952; exited: -; ]
Jun-07 09:07:05.185 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=validate_sample_sheet; work-dir=/tmp/powry48p-wf-transcriptomes-work/94/bc915a67142cdc607ba4b15072b42f
error [nextflow.exception.ProcessFailedException]: Process validate_sample_sheet terminated for an unknown reason -- Likely it has been terminated by the external system
Jun-07 09:07:05.186 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 489574; id: 6; name: pipeline:differential_expression:ch
eckSampleSheetCondition; status: RUNNING; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/44/e480a37028ef62b58ef456a9fcfade started: 1717707598953; exited: -; ] -- exitStatu
sReadTimeoutMillis: 270000; delta: 271254
Current queue status:
job: 486434: RUNNING
Content of workDir: /tmp/powry48p-wf-transcriptomes-work/44/e480a37028ef62b58ef456a9fcfade
null
Jun-07 09:07:05.186 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 489574; id: 6; name: pipeline:differential_expression:checkSampleSheetCondition;
status: COMPLETED; exit: -; error: -; workDir: /tmp/powry48p-wf-transcriptomes-work/44/e480a37028ef62b58ef456a9fcfade started: 1717707598953; exited: -; ]
Jun-07 09:07:05.186 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=pipeline:differential_expression:checkSampleSheetCondition; work-dir=/tmp/powry48p-wf-transcriptomes-work/44/e480a37028ef62b58ef456a9fcfade
error [nextflow.exception.ProcessFailedException]: Process pipeline:differential_expression:checkSampleSheetCondition terminated for an unknown reason -- Likely it has been terminated by
the external system
Jun-07 09:07:05.187 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop
Jun-07 09:07:05.488 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=6; ignoredCount=0; cachedCount=0; pendingCount=0; submittedC
ount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=1h 3m 55s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=6; peakCpus=9; peakMemory=41 G
B; ]
Jun-07 09:07:05.488 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Jun-07 09:07:05.489 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Jun-07 09:07:05.828 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Jun-07 09:07:05.884 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jun-07 09:07:05.903 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
Ask away!
Hello, Professor I am running the workflow, but it was killed with the error: `ERROR ~ Error executing process > 'pipeline:preprocess_ref_annotation'
Caused by:
Process
pipeline:preprocess_ref_annotationterminated with an error exit status (126)Command executed:
sed -i -e 's/transcript_id "";//g' 1.Ma.rename.gtf
mv 1.Ma.rename.gtf "amended.1.Ma.rename.gtf"` I guess this is due to my uncorrected annotation file (gff） and I also noticed " A reference annotation in GFF2 or GFF3 format (extensions .gtf(.gz), .gff(.gz), .gff3(.gz)). Only annotation files from Encode, Ensembl and NCBI are supported" in the ReadMe. So are there any suggestions that help me to convert my annotation file to the required format. Thanks very much.