Hello:
I am following the MiSeq SOP using mothur v.1.48.5 (pre-compiled). Everything is going well until I get to the chimera.vsearch step. It appears that the remove.seqs command is not updating the count table that I provided. The relevant segment of the logfile is provided below.
I think I could work around this using the removechimeras option, followed by remove.seqs:
chimera.vsearch(fasta=current, count=current, dereplicate=t, removechimeras=f)
remove.seqs(fasta=current, count=current, accnos=current)
I just wanted to check in to see if I am calling chimera.vsearch incorrectly.
Thank you,
Jim
mothur > chimera.vsearch(fasta=current, count=current, dereplicate=t)
Using bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.count_table as input file for the count parameter.
Using bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter.
Using 28 processors.
Using vsearch version v2.16.0.
Checking sequences from bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.fasta …
When using template=self, mothur can only use 1 processor, continuing.
It took 269 secs to check your sequences. 162586 chimeras were found.
Removing chimeras from your input files:
/******************************************/
Running command: remove.seqs(fasta=bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.fasta, accnos=bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos)
Removed 162586 sequences from bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.fasta.
Output File Names:
bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.pick.fasta
/******************************************/
Output File Names:
bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.chimeras
bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos
bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta
mothur > summary.seqs(fasta=current, count=current)
Using bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.count_table as input file for the count parameter.
Using bc_enrich.trim.contigs.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta as input file for the fasta parameter.
Using 28 processors.
[ERROR]: Your count file contains 187867 unique sequences, but your fasta file contains 25281. File mismatch detected, quitting command.