Problem with groupfile in unifrac.weighted

mothur bugs
1

Hello,

I have had no issues previously with using the OTU commands to generate diversity metrics etc. I am now trying to use Unifrac through the mothur platform, but keep getting name errors that end my session.

My input is:

mothur > unifrac.unweighted(distance=lt, random=F, tree=file.final.phylip.tre, name=file.final.names, group=file.final.groups)

When I run the command, I receive the following message:

Name: ZYEY6 is not in your groupfile, and will be disregarded.
Name: is not in your groupfile, and will be disregarded.
error with lc
Name: 8I3I6 is not in your groupfile, and will be disregarded.
Name: Q595G is not in your groupfile, and will be disregarded.
ZYEY6 is not in your name file, please correct.
logout

[Process completed]

For some reason it is asking for partial names - only the first 5 letters. I have looked at the three input files, and all of my names are written in the format ‘ZYEY6:664:576’, and are separated by commas. None are only the first 5 letters as the message suggests. I have had no difficulty with other commands.

Any help would be appreciated!

2

The ‘:’ character is a special character in trees used to indicate a branch length will follow. Try replacing the ‘:’ characters in your sequence names.

3

That was the issue. I really appreciate the quick reply!

Thanks.