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Published 20 hours ago • verified publisher icon galaxyproject

Metagenome assembly tutorial "broken"?

Open bernt-matthias opened this issue 10 months ago • 0 comments

The QC step of the tutorial suggests to upload the html results of QUAST.

This does not work: https://github.com/galaxyproject/galaxy/issues/19220 also the results are not available as data library (or I have not found it).

In my tests the QUAST step took 5 hours and failed for some of the datasets, since it downloads reference genomes from NCBI which seems to fail from time to time (as in this super old issue).

  • Restarting quast seems possible, but problematic for the multi-output tool, i.e. one one gets one updated output. Maybe this might work out if combined with MultiQC
  • Maybe replace QUAST by CheckM?

bernt-matthias avatar Nov 29 '24 08:11 bernt-matthias