Closed semiller10 closed 11 months ago
Thanks, again, for catching this @semiller10. I took your advice and implemented the reannotation of all databases in the self test. Since it can take a really long time, I also added multi-threading capacity to the anvi-self-test
program to speed things along a bit. But setting up KEGG data also takes so much time at this point (19 minutes in my current run of anvi-self-test --suite metabolism
) that the extra overhead from reannotation doesn't really matter anyway, I guess :)
Short description of the problem
Test genomes used for metabolism estimation in
anvi-self-test --suite metabolism
have contigs databases that contain KEGG annotations from a modules database that is not up-to-date with the current KEGG snapshot.anvi'o version
Detailed description of the issue
An error is thrown because the modules db hash is inconsistent between the test genome contigs db and the new modules db built in the test run from the latest KEGG snapshot. The obvious solution is to update the KEGG annotations of the anvi'o sandbox contigs dbs, but perhaps a better solution would be to reannotate the copies of the contigs dbs used in the test script by running
anvi-run-kegg-kofams
in the script. This would prevent future discrepancies between modules dbs built in the script from an up-to-date KEGG snapshot and out-of-date contigs db annotations.