I wanted to remove chimeras from a sample of amplicon 16S reads. The 7,000 sequences are in a FASTA file. The following command:
mothur "#chimera.uchime(fasta=/tmp/tmp773clwju/reads.fasta,reference=self,chunks=16,chimealns=T,abskew=1)"
Produces these files:
/tmp/tmp773clwju/reads.count_table
/tmp/tmp773clwju/reads.unique.fasta
But no file ending with “accos” and apparently no output from the chimera detection process at all. Any ideas what this is due to?
The log contains this:
[NOTE]: Setting random seed to 19760620.
Script Mode
mothur > chimera.uchime(fasta=/tmp/tmp773clwju/reads.fasta,reference=self,chunks=16,chimealns=T,abskew=1)
Using 8 processors.
uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.
Checking sequences from /tmp/tmp773clwju/reads.fasta ...
When using template=self, mothur can only use 1 processor, continuing.
No count file given, running unique.seqs command to generate one.
/******************************************/
Running command: unique.seqs(format=count, fasta=/tmp/tmp773clwju/reads.fasta)
7651 7567
Output File Names:
/tmp/tmp773clwju/reads.count_table
/tmp/tmp773clwju/reads.unique.fasta
/******************************************/
mothur > quit()
Trying the command again with the new files created as input, i.e. pair of count_table
and unique
files like this mothur "#chimera.uchime(fasta=/tmp/tmp773clwju/reads.unique.fasta,count=/tmp/tmp773clwju/reads.count_table,reference=self,chunks=16,abskew=1)"
doesn’t create any output either.
I’m using mothur v.1.42.1. Thanks.