Hello, I am a new user to mothur working through a piece of sequence data and having some concerns regarding the uchime and its output files. I am expecting that since in the MiSeq SOP it mentions a count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table based file that I assume should come out of uchime but following the SOP I do not get the related .uchime.pick.count_table file anywhere. Although this doesn’t stop the later code requiring the .uchime.pick.coun_table file as a component it gives an error message regarding being unable to open the file and that it is disregarding it. I’m hoping someone can point me in the direction of what I may be missing, thanks.
Checking sequences from SRD1B.trim.contigs.good.unique.good.filter.unique.precluster.fasta …
When using template=self, mothur can only use 1 processor, continuing.
It took 5 secs to check 710 sequences. 8 chimeras were found.
The chimera.uchime (and all chimera detection commands in mothur) don’t remove sequences from your data, just flag the ones mothur thinks are chimeric and outputs a list of them in the accnos file. Once you put these through the remove.seqs command you’ll get the *.pick.fasta and *.pick.count_table files.
Hey thanks for the response, I ran the code and got this:
Removed 8 sequences from your fasta file.
Removed 10 sequences from your count file.
Output File Names:
SRD1B.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta
SRD1B.trim.contigs.good.unique.good.filter.unique.precluster.pick.count_table
In the MiSeq SOP after the remove.seqs and a summary.seqs it has this with the .uchime in the .count_table file
Alright, nevermind, I was attempting to run through without a .files file from the start and was instead using the ffastq and rfastq as the beginning point for make.contigs, after organizing multiple fastqs into a .files and running that I had no issues.