The update to 1.47 from group files to count files seems to have caused my batch file and automated pipeline to really crash. I updated my commands that were using group= to now use count=, but
unique.seqs() still seems to lump all samples together due to a loss of group information.
mothur > make.shared(list=current, count=current, label=0.03)
Using /mnt/storage/labs/emerson/Arctic/Seqs/toolgt_small/out/rssm.trim.contigs.good.unique.good.filter.unique.precluster.pick.count_table as input file for the count parameter.
Using /mnt/storage/labs/emerson/Arctic/Seqs/toolgt_small/out/rssm.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.opti_mcc.list as input file for the list parameter.
[WARNING]: Your count file does not have group info, all reads will be assigned to mothurGroup.
I looked at some of my count_table files created early in the process and it looks like they lost their group information. Any thoughts about this?