Question: Filter FASTQ by length job "currently running" for 24+ hrs.
gravatar for christopher.ray
9 months ago by
christopher.ray0 wrote:


I am using Galaxy. I have a library of small RNA in FASTQ format that I am trying to filter by size. The file has around 38,000,000 reads and is 5.5GB. The Galaxy tool I used was "Filter FASTQ reads by quality score and length". I want to discard all reads that fall outside the range of 19-25 bases long.

This is my first time using the tool, but I'm fairly sure I have input the few simple parameters correctly. I have tried restarting the job a few times and have left one attempt going for 24 hours+. It takes a couple minutes to move from grey (in queue) to yellow (in progress), but stays on that stage for hours and never completes.

Is this usual behaviour? Anything I can do to troubleshoot? Is there another tool in Galaxy that will filter my FASTQ file by read size?

Thankyou for any suggestions!

slow stuck fastq filter • 220 views
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