combine count & groups file?

I have something which feels like it would be rather easy to solve:

I have followed the MiSeq SOP and used a count file instead of a names file.

Just before make.shared, I partition my total dataset into subsets using get.seqs(list, count, taxonomy, accnos) (see below).

For each subset I have created a groups file which pools over replicates. In make.shared I use the groups file together with the subsetted list file. In doing so, I do not “bring” all sequences. Looking at the below example, the OTUs in the produced shared file has a sum of 214184 sequences instead of 17470562.

I guess I would like to combine the information in my count file with that of my group file (as count files can have group information), but again, I do not have a names file which matches my count file so I can’t run count.seqs(names, groups). Obviously creating one using unique.seqs wont do it.

This feels like it shouldn’t be a problem… Any advice is much appreciated!


mothur > get.seqs(list=496_515_seqs_2Bjork.small.pick.pick.unique.align.good.pick.filter.unique.pick.trim.pick.fn.unique_list.list, accnos=solo.instant.accnos, count=496_515_seqs_2Bjork.small.pick.pick.unique.align.good.pick.filter.trim.pick.count_table,

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

Selected 17470562 sequences from your count file.
Selected 214184 sequences from your list file.
Selected 214184 sequences from your taxonomy file.

Output File Names: 

Have you tried using merge.groups instead of your home-brew approach?