I was trying to do chimera removal using chimera.vsearch command but it does not detect any chimeras and does not create any count_table and fasta files. I got the following error message when the command got finished running.
(im an undergrad and a bit unexperienced with mothur so any help would be highly appreciated) (this is part of a mock test so I know that there should be chimeras that need to be removed)
mothur > chimera.vsearch(fasta=Cecum_sample.good.unique.good.filter.unique.fasta, count=Cecum_sample.good.unique.good.filter.count_table, diffs=2)
[WARNING]: diffs is not a valid parameter, ignoring.
The valid parameters are: reference, fasta, name, count, group, processors, seed, inputdir, outputdir, abskew, uchimealns, removechimeras, minh, mindiv, xn, dn, mindiffs, vsearch, and dereplicate.
Using 4 processors.
Checking sequences from Cecum_sample.good.unique.good.filter.unique.fasta …
When using template=self, mothur can only use 1 processor, continuing.
vsearch v2.16.0_win_x86_64, 3.9GB RAM, 4 cores
Reading file Cecum_sample.good.unique.good.filter.unique.temp 100%
0 nt in 0 seqs
minseqlength 1: 1 sequence discarded.
Sorting by abundance 100%
Counting k-mers 100%
Detecting chimeras 100%
Found 0 chimeras, 0 non-chimeras,
and 0 borderline sequences in 0 unique sequences.
Taking abundance information into account, this corresponds to
0 chimeras, 0 non-chimeras,
and 0 borderline sequences in 0 total sequences.
It took 1 secs to check your sequences. 0 chimeras were found.
No chimeras found, skipping remove.seqs.
Output File Names: