I’ve recently updated v .1.42.3 and I am having some issues with data processing. For example, pcr.seq command doesnt generate a name.file (although this could be put down to the fact that there’s no sequences to trim, so I could recycle the last name file). However, running precluster command, mothur doesnt generate a name file either and the output is one pick.fasta and one count.table (even if I’m not working with groups but with individual samples). Therefore, my new fasta file doesnt match my old name file and I cant continue the processing.
Does anybody know what might be happening or if this could be due to the new version of mothur??
Thank you in advance!
Can you post the exact command syntax for how you’re running pcr.seqs? The output of pre.cluster will be a count file, replacing the names file.
The exact command for pcr.seq is: pcr.seqs(fasta=P1A1stability.trim.contigs.good.unique.align, name=P1A1stability.trim.contigs.good.names, start=0, end=18929, keepdots=F, processors=4). As for replacing the name file for a count file whe runnin pre.cluster, I would be losing the names of redundant sequences, isn’t it possible to have a name file output?
The pre.cluster command no longer outputs a name file. We made this change to improve performance and reduce file sizes. You can convert a count file to a name file. The original names are not used, but a name is generated for each redundant sequence. For example:
seq1 3 3
would become something like
seq1 seq1,seq1_1,seq1_2
Is there a reason you need the specific sequence names? Perhaps there is a workaround that will get you what you are looking for?