InterProScan job running for 10 days on usegalaxy.eu – is this normal?

1

Hello,

I am running an InterProScan analysis, and my job has been running for about 10 days without completing.

Here are some details:

  • Tool: InterProScan
  • Input: proteome dataset
  • File size: ~50 MB (FASTA format/ .fa)
  • Runtime: ~10 days

I would like to know if this runtime is normal for this type of dataset or if my job might be stalled or facing an issue.

Could you please advise whether I should wait longer, cancel and re-run, or adjust any parameters to improve performance?

Thank you for your help!

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2

Hi @Santosh_Lavhale,

The run time is on higher side, but this is based on my experience with Galaxy Australia. Europe may have different setup for InterProScan jobs. Maybe keep the job for now but check the input file to confirm it has amino acid sequences. Check the job setup, especially mode (nucleotide or protein). If you have amino acid sequences, the mode should be protein.

The input file is someone big for proteome. Check it for presence (nearly) identical sequences. It is not uncommon to see files containing dozens identical sequences. If you use unique sequences, run time will be smaller.

Sometimes Galaxy does not update job status. Refresh history or Galaxy window (click at Galaxy icon at the top left corner).

Kind regards,

Igor

3

Hi Igor,

Thank you very much for your suggestions. I checked the input file, which contains amino acid sequences (proteome data), and its size is approximately 50 MB. The history has been refreshed, and it shows that the job is currently running.

Best Regards,

-Santosh