remove.seqs didn't remove any from count

Commands in mothur
1

When I’m running make.shared I’m getting the

[ERROR]: M01676_22_000000000-ANR1V_1_1104_10006_15172 is in your groupfile and not your listfile. Please correct.

thousands of times. I think it has to do with removing chimeras

mothur > remove.seqs(fasta=current, accnos=current, count=current)
Using bb16.trim.contigs.good.unique.good.filter.precluster.denovo.uchime.accnos as input file for the accnos parameter.
Using bb16.trim.contigs.good.unique.good.filter.precluster.denovo.uchime.pick.count_table as input file for the count parameter.
Using bb16.trim.contigs.good.unique.good.filter.precluster.fasta as input file for the fasta parameter.

[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.

Removed 428918 sequences from your fasta file.
Removed 0 sequences from your count file.

Output File Names: 
bb16.trim.contigs.good.unique.good.filter.precluster.pick.fasta
bb16.trim.contigs.good.unique.good.filter.precluster.denovo.uchime.pick.pick.count_table

Shouldn’t chimeras be removed from the count table as well?

2

We remove them directly from the count file in chimera.uchime - how did you run chimera.uchime?

3

Huh, clearly haven’t been examining my logfiles closely enough. Never noticed that they were always “0 removed from countfile”

chimera.uchime(fasta=current, count=current, dereplicate=t)

Must have just been something weird with that run, I reran the batch from just after ^ and didn’t get the error this time.