I have been unfortunate enough to include hyphens in the group names defined in my oligos file:
barcode TAGTATCAGC fjord11-MID09
barcode CATAGTAGTG blank11-MID13
barcode CGTCTAGTAC NP11-MID17
barcode TACTCTCGTG NPSi11-MID23
I have not experienced that this has been problematic until I tried to use get.groups() to pull out sequences from specific groups. When I try to extract sequences from, for example, group “NP11-MID17”, I get the following error:
mothur > get.groups(group=mes_cop_final.groups, name=mes_cop_final.names, fasta=mes_cop_final.fasta, groups=NP11-MID17)
MID17 is not a valid group, and will be disregarded.
NP11 is not a valid group, and will be disregarded.
You provided no valid groups. I will run the command using all the groups in your groupfile.
Selected 28868 sequences from your name file.
Selected 1149 sequences from your fasta file.
Selected 28868 sequences from your group file.
Output File names:
I tried also to use “” to contain the group name and got the same error message. So it seems that the hyphen is interpreted as a group separator regardless, which means that none of my group names make any sense. Have I just been unlucky here and need to change my group names to exclude the hyphen and rerun everything or is there a workaround?
Thanks in advance