Uchime Output file: count_table

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.

What I did in mothur from the log file;

mothur > chimera.uchime(fasta=SRD1B.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=SRD1B.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)

Using 8 processors.

uchime by Robert C. Edgar
This code is donated to the public domain.

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.

Output File Names:


Just run

remove.seqs(fasta=SRD1B.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=SRD1B.trim.contigs.good.unique.good.filter.unique.precluster.count_table, accnos=SRD1B.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnos)

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: 

In the MiSeq SOP after the remove.seqs and a summary.seqs it has this with the .uchime in the .count_table file

classify.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)

I’m wondering if the .uchime is supposed to be there?

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.