Utilizing galaxy space effectively

Hi I am new to galaxy, so if someone has asked this question in the past I apologize. I downloaded 42 files to galaxy via the SRA run selector as a collection. I now have my FASTQ files and would like to use Trimmomatic; however, I am above the alloted space quota. Trimmomatic was run on the first 15 files already and the rest are waiting to be processed.

My question is if I delete/purge the first 15 files in the collection ( FASTQ) will that allow Trimmoatic to resume or will it mess things up because the data is grouped together as a collection. I just not sure and it took forever to download so any advice would be much appreciated.

Hi @LittleBlueHeron

One solution is to break out the read data into distinct collections during download and processing in batches.

  • Trimmomatic creates near duplicate very large fastq outputs.
  • The idea would be to get through that step with a portion of the data, purge the original files, repeat with another portion, then combine the results into one collection for downstream processing.
  • From your description it seems like 2-4 batches would be enough.

Another is to make a small short-term extra quota request (extra 100-250 GB for a few days to a week).

If that is not enough help, would you please post back a share link to this history? That context will help with review and specific solutions. :slight_smile:


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