How big can your template file be for classify.seqs? I made a custom fasta file from silva that included ~13K sequences, and classify.seqs first paralyzed my machine (Linux w/ 4G of RAM) and then barfed with “Error: St9bad_alloc has occurred in the PhyloTree class function addSeqToTree.” The file was an aligned fasta file of 18S sequences - could that be part of the problem? (An addition to the classify.seqs wiki page describing the expected format of the template file would be good.)
thanks,
Bill
The size of the template file should be fine. It sounds like a problem with the taxonomy file, not the template file. We added alot more error checking on the taxonomy file in version 1.11.0. The most common reason for a bad_alloc in the read was missing a ;.
I seem to be getting the same behavior regardless of what tax file I use (even the one I downloaded from the mothur site). I will try it on a different machine.
If you send your customized template and taxonomy files to mothur.bugs@gmail.com I can take a look.
On a different machine I was initially having the same problem, but then (as you suspected) I found a missing semi-colon in my tax file. I will re-try the other machine to see if that was the problem there as well. Thanks for the tip.