mothur

Chimera.uchime does not produce any output

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.

Our latest version is available here, https://github.com/mothur/mothur/releases/tag/v1.44.2. Can you give it a try?

I suspect mothur is unable to find the uchime program. In our current version you can specify the location of the uchime executable and / or set a location for mothur’s external tools.

mothur > set.dir(tools=pathToUchime)

or

mothur > chimera.uchime(fasta=reads.fasta,chunks=16,chimealns=T,abskew=1, uchime=pathToUchime/uchime)

If this does not solve the problem, can you run the command in debug mode with a fasta and count file and post the results.

mothur > set.dir(tools=pathToUchime, debug=true)

mothur > unique.seqs(fasta=reads.fasta, format=count)

mothur > chimera.uchime(fasta=current, count=current, chunks=16,chimealns=T,abskew=1)

Kindly,
Sarah