Hi,
The remove.groups command removes different number of sequences from the fasta file when a .names file is included. This is an example:
When a .names file is not included
mothur > remove.groups(fasta=MCM.final5.fasta, group=MCM.final5.groups, groups=C1-C7-C25-N10-N22)
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is MCM.final5.pick.names which seems to match MCM.final5.fasta.
Removed 8300 sequences from your fasta file.
Removed 427773 sequences from your group file.
Output File names:
MCM.final5.pick.fasta
MCM.final5.pick.groups
When a .names file included
mothur > remove.groups(fasta=MCM.final5.fasta, name=MCM.final5.names, group=MCM.final5.groups, groups=C1-C7-C25-N10-N22)
Removed 427773 sequences from your name file.
Removed 7588 sequences from your fasta file.
Removed 427773 sequences from your group file.
I am nor sure if this is a bug or I am wrong somewhere!
Regards
Nezar Al-hebshi