Hi,
The remove.groups command removes different number of sequences from the fasta file and count table file
This is an example:
mothur > remove.groups(count=exp44_65samples.trim.contigs.subsample.unique.good.filter.unique.precluster.count_table, fasta=exp44_65samples.trim.contigs.subsample.unique.good.filter.unique.precluster.fasta, groups=exp44_b3m0_020423_-exp44_b1m3_060423r-exp44_b5m0_270323r-exp44_b1m2_290323r-exp44_b1m2_040423r)
Output File names:
exp44_65samples.trim.contigs.subsample.unique.good.filter.unique.precluster.pick.count_table
exp44_65samples.trim.contigs.subsample.unique.good.filter.unique.precluster.pick.fasta
mothur > summary.seqs(fasta=exp44_65samples.trim.contigs.subsample.unique.good.filter.unique.precluster.pick.fasta, count=exp44_65samples.trim.contigs.subsample.unique.good.filter.unique.precluster.pick.count_table)
[ERROR]: Your count file contains 69791 unique sequences, but your fasta file contains 69790. File mismatch detected, quitting command.
I tried more than once and did the analysis from the beginning but the bug continues.
I tried doing summary.seqs without removing the sequences and it works.
So I believe the bug is in remove.groups
Best regards,
Debora