mothur

memory problems with classify.seqs()

Hi,

I’ve been having some problems with classify.seqs() and large training sets in mothur 1.15. These same training sets used to result in mothur 1.12 using about 2GB memory, and everything functioned great. Now, when it gets to the “Calculate template probabilities” step, instead of climbing to 2GB memory, it climbs to 11GB memory plus another 23GB in virtual memory. It crashed the computer a few times, and caused a restart. (Mac OS X 10.5) I’m not sure what has changed in handling memory from 1.12 to 1.15, but it must be a bug of some kind I imagine.

Thanks,
Jeff

Hmm… I reverted to an old version of mothur, and it looks like my memory problems are still there. I guess my training set has changed – I added another level of taxonomic depth (to identify the accession number of the sequence it matched, if there was one best match). I guess I didn’t think about the effect that would have on memory… quite large!

Can you tell me how you added that extra level of taxonomic depth (to identify the accession number of the sequence it matched, if there was one best match)?. I have a final list of OTUs (which a fromer group member of mine generated) and their abundances along with their taxa names (up until family-level) and now I’m scratching my head over how to append SILVA taxon accession numbers to this final list. I’m new to mothur and this is why I’m asking this question