Parsimony output: removing groups error message

Commands in mothur
1

Dear Forum,

When my design.file is setup as in Example 1, I get an error that my diet has been removed (Example 1 Output) . But when I setup my design file like Example 2, I don’t get an error message (Example 2 Output). I also get different ParsSig values between the outputs, but not by very much. Can someone explain if I should be setting up my group files like Example 1 or 2, and why the significant values would differ?

Thanks,
Ryan

Example 1
group diet
1Small Cheeseburgers
2Small Cheeseburgers
3Small Snickers
4Small Snickers
5Small Skittles
6Small Skittles
7Small Hotdogs
8Small Hotdogs
9Small Hotdogs
10Small Hotdogs

Example 2
1Small Cheeseburgers
2Small Cheeseburgers
3Small Snickers
4Small Snickers
5Small Skittles
6Small Skittles
7Small Hotdogs
8Small Hotdogs
9Small Hotdogs
10Small Hotdogs

Example 1 Output
mothur > parsimony(tree=GI.an.thetayc.0.03.lt.ave.tre, group=mouse.diet.design, groups=all)

Using 8 processors.

Removing group: diet because all sequences have been removed.
********************###########
Comparing to random:||||||||||||||||||||||||||||||||||||||||||||||||||||

Tree# Groups ParsScore ParsSig
1 Hotdogs-Snickers 1 <0.001

1 Hotdogs-Cheeseburgers 3 0.277

1 Snickers-Cheeseburgers 1 0.002

1 Hotdogs-Skittles 2 0.006

1 Snickers-Skittles 2 0.026

1 Cellulose-Skittles 2 0.097



Example 2 Output mothur > parsimony(tree=GI.an.thetayc.0.03.lt.ave.tre, group=mouse.diet.design, groups=all)

Using 1 processors.
********************###########
Comparing to random:||||||||||||||||||||||||||||||||||||||||||||||||||||

Tree# Groups ParsScore ParsSig
1 Hotdogs-Snickers 1 <0.001

1 Hotdogs-Cheeseburgers 3 0.318

1 Snickers-Cheeseburgers 1 0.008

1 Hotdogs-Skittles 2 <0.001

1 Snickers-Skittles 2 0.02

1 Cellulose-Skittles 2 0.102

2

What version of mothur are you using?

3

mothur/1.38.1

4

Can you send your input files to mothur.bugs@gmail.com?

5

You should get them, if you haven’t already.

6

When you enter a design file under the ‘group’ parameter it can’t have the header line. Mothur assumes since the file has been entered as a group file, that it will not contain the header. This is a bit confusing. I will add it to our list to add a design parameter to the parsimony and unifrac commands to clear things up.