Segmentation fault w/ count.groups


i’m using the latest version on a Mac OS X (Mountain lion).
I’ve ran an analysis according to the SOP, following most of the recommended settings.

After make.shared (where it seems I used an earlier groups file but still endded up getting the right number of sequences) I get a shared file but can’t count groups (I could count before, somehow, probably based on 0.15 and not 0.05, since I didn’t have a shared file). it seems like the shared file is made at the beginning of make.shared but then deleted straight after, for some reason. trying count.groups ended with the following -

mothur > count.groups()

Using /Users/gils/documents/seqanalysis/output/ as input file for the shared parameter.
[ERROR]: Could not open /Users/gils/documents/seqanalysis/output/
Segmentation fault: 11

(just to show I have a shared file -

Your group file contains 490387 sequences and list file contains 433718 sequences. Please correct.

Output File Names:

Is this due to the difference in seq numbers between my groups and list?

and a suggestions - it might be helpful to generate an additional accnos file for sequences that are absent in one of the two files so that it can be removed from the list/group (or any) file. or, it could be made into a QC type of a command where you can compare different types of files (e.g, list/shared with groups) and omit any discrepancies between the two. I now you can do it using list, then get.seqs… I just think this would be more straight forward.



**Update - using list and group files that had the same number of sequences generated a shared file that was not automatically deleted and prevented the segmentation fault.