read.otu error message

Commands in mothur
1

I am analyzing 454 sequences and I have ~ 5000 sequences in 12 groups. I followed the analysis described for the Sogin dataset.

For:
mothur > read.otu(list=Atacama.unique.pick.filter.fn.list, group=Atacama.pick.groups, label=unique-0.03-0.05-0.10)

I get the following message:
Your group file contains 39300 sequences and list file contains 35460 sequences. Please correct.
For a list of names that are in your group file and not in your list file, please refer to Atacama.unique.pick.filter.fn.missing.name.

The Atacama.unique.pick.filter.fn.missing.name does not contain any name (see attached) and I this point I do not know what to do.

Help!

2

Would you mind sending the logfile and your list and group files to mothur.bugs@gmail.com?

3

Thanks for the files, it seems the problem lies in your group file. The group file mothur needs for analysis consists of 2 tab separated columns. The first column holds the sequence name, and the second column contains the sequence’s group.

For example:
AY457912 A
AY457911 A
AY457910 A
AY457909 B
AY457908 B
AY457907 B
AY457904 C
AY457903 C
AY457902 C