ARRIBA_VISUALISATION : Process exceeded running time limit (8h)

[ZheFrench]

Description of the bug

Process exceeded running time limit of (8h) for visualisation.

That's weird it's taking so long. It was a recurrent one. I don't know if it's worth increasing running time here or it's just freezing indefinitely.

I finally ended up to set -resume with --skip_vis will to avoid the error. WRONG ANSWER : It will create only an empty fill for fusion report...

nov.-28 04:52:27.079 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (E5087.normal); work-dir=/data2/USERS/villemin/Myelome/fusion/work/7f/37152b0171cbe2c7bf012aabf78b73
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (E5087.normal)` failed
nov.-28 04:52:27.160 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (E5087.normal)'

Caused by:
  Process exceeded running time limit (8h)

Command executed:

  draw_fusions.R \
      --fusions=E5087.normal.FusionInspector.fusions.tsv \
      --alignments=E5087.normal.Aligned.sortedByCoord.out.bam \
      --output=E5087.normal_combined_fusions_arriba_visualisation.pdf \
      --annotation=Homo_sapiens.GRCh38.109.chr.gtf \
       --cytobands=cytobands_hg38_GRCh38_v2.3.0.tsv \
      --proteinDomains=protein_domains_hg38_GRCh38_v2.3.0.gff3 \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION":
      arriba: $(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version: //')
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Command error:
  Drawing fusion #1319: TKT:UBE2E3
  Drawing fusion #1320: TM7SF3:FAR2
  Drawing fusion #1321: TMBIM1:DTX2
  Drawing fusion #1322: TMC6:RUNX3
  Drawing fusion #1323: TMCC3:DNAJC5
  Drawing fusion #1324: TNFAIP8:HSD17B4
  Drawing fusion #1325: TNFAIP8:ITK
  Drawing fusion #1326: TNFAIP8:MATR3
  Drawing fusion #1327: TNFRSF10B:EGR3
  Drawing fusion #1328: TNFRSF10C:HNRNPH3
  Drawing fusion #1329: TNFRSF10C:ISCA1
  Drawing fusion #1330: TNFRSF1B:TGIF2
  Drawing fusion #1331: TNFSF10:PICALM
  Drawing fusion #1332: TNIP2:SET
  Drawing fusion #1333: TNKS:NUDCD1
  Drawing fusion #1334: TNRC18:BRI3
  Drawing fusion #1335: TNRC18:EEF1D
  Drawing fusion #1336: TNRC6A:TPM3
  Drawing fusion #1337: TOLLIP:ACAP3
  Drawing fusion #1338: TOR1AIP2:SECISBP2L
  Drawing fusion #1339: TPI1:CASTOR1
  Drawing fusion #1340: TPI1:RBM4
  Drawing fusion #1341: TPK1:ARHGAP15
  Drawing fusion #1342: TPM3:UBAP2L
  Drawing fusion #1343: TPM4:LPAR2
  Drawing fusion #1344: TPM4:NSD3
  Drawing fusion #1345: TPM4:R3HDM4
  Drawing fusion #1346: TPM4:RBM38
  Drawing fusion #1347: TPR:ACAP2
  Drawing fusion #1348: TRA2B:FUS
  Drawing fusion #1349: TRAF2:TSC22D3
  Drawing fusion #1350: TRAF3:HP1BP3
  Drawing fusion #1351: TRAF7:ATP6V0C
  Drawing fusion #1352: TRAM2:MYH9
  Drawing fusion #1353: TREM1:BAZ1A
  Drawing fusion #1354: TREM1:KCTD20
  Drawing fusion #1355: TREM1:TMEM71
  Drawing fusion #1356: TSEN34:SH3BP2
  Drawing fusion #1357: TSNARE1:SELENOO
  Drawing fusion #1358: TSPAN4:TNK2
  Drawing fusion #1359: TTYH3:AKT1
  Drawing fusion #1360: TUBA1A:LPCAT1
  Drawing fusion #1361: TUBB:CNIH4
  Drawing fusion #1362: TUBGCP6:ANKLE2
  Drawing fusion #1363: TVP23C:TTC39C
  Drawing fusion #1364: TXLNG:PLP2
  Drawing fusion #1365: TXNIP:QRICH1
  Drawing fusion #1366: TYROBP:TLR2
  Drawing fusion #1367: TYW3:NRDC
  Drawing fusion #1368: U2AF1:ACAP2

Work dir:
  /data2/USERS/villemin/Myelome/fusion/work/7f/37152b0171cbe2c7bf012aabf78b73

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Command used and terminal output

No response

Relevant files

nextflow.log

System information

Nextflow version (eg. 23.04.0) Hardware : HPC Executor : local Container engine: Singularity OS : Linux Ubuntu Version of nf-core/rnafusion 2.4