I keep running into errors with the metagenomic classifer GOTTCHA. Can anybody offer some suggestions?
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10 months ago


I am doing a metagenomic benchmarking test and for this I want to run the GOTTCHA classifier on 20 in silico generated samples from the CAMI challenge (human toy gastrooral to be exact). Interestingly, GOTTCHA can classify 15 out of the 20 samples without error, but for the rest, it returns 0 species. The problem comes from the splitrim script that returns 0 splitrimmed reads (out of 30 million). I found this hard to believe, so I am trying to locate the problem right now. The detailed error messages can be found in this github issue: https://github.com/LANL-Bioinformatics/GOTTCHA/issues/18

The github repository seems to be abandoned, that's why I am writing here, hoping that maybe somebody has a solution for the problem.

Thanks, Bertalan Tak√°cs

gottcha classification metagenomics • 438 views

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