Troubleshooting an error (exit code 1) when performing BWA-MEM2 on WGS data

usegalaxy.org support
3

Hi @edf393

The FAQs explain what you can do in general to continue working at a public Galaxy server. In short: use an indexed genome as the mapping target (bosTau8 instead) + split the query reads into a collection, run some QA, map, then merge the results.

Or, you can consider setting up a private Galaxy server with scaled up resources.

Details:

  • The job failed for exceeding memory limits at the public Galaxy server FAQ.
  • Specifically:
    • The fastq datasets are too large – ~25 GB compressed per end. FAQ
    • The fasta custom genome is too large, plus has a formatting problem. FAQ