split.abund group files with more than one label

mothur bugs
1

When I run split.abund with more than one label, and then try to read.otu on only one of those labels, there is a problem:

split.abund(fasta=yagu.stakes.fasta, list=./yagu.stakes.list, group=yagu.stakes.groups, cutoff=1, label=0.01-0.03)

Output File Names: 
./yagu.stakes.rare.list
./yagu.stakes.abund.list
./yagu.stakes.0.01.rare.groups
./yagu.stakes.0.01.abund.groups
./yagu.stakes.0.01.rare.fasta
./yagu.stakes.0.01.abund.fasta
./yagu.stakes.0.03.rare.groups
./yagu.stakes.0.03.abund.groups
./yagu.stakes.0.03.rare.fasta
./yagu.stakes.0.03.abund.fasta


read.otu(list=yagu.stakes.abund.list, group=yagu.stakes.0.01.abund.groups, label=0.01)

Output File Names: 
yagu.stakes.abund.GuS1.rabund
yagu.stakes.abund.GuS2.rabund
yagu.stakes.abund.GuS3.rabund
yagu.stakes.abund.GuS4.rabund
yagu.stakes.abund.GuS5.rabund
yagu.stakes.abund.GuS6.rabund
yagu.stakes.abund.YaS1.rabund
yagu.stakes.abund.YaS3.rabund
yagu.stakes.abund.YaS5.rabund
yagu.stakes.abund.YaS6.rabund
yagu.stakes.abund.YaS8.rabund
yagu.stakes.abund.shared

read.otu(list=yagu.stakes.abund.list, group=yagu.stakes.0.03.abund.groups, label=0.03)

Your group file contains 1322 sequences and list file contains 1275 sequences. Please correct.
For a list of names that are in your group file and not in your list file, please refer to yagu.stakes.abund.missing.name.

There is a mismatch with the list file and the group file ie read.otu is trying to match the group file to the 0.01 line in the list file even though I’ve specified the 0.03 label and the 0.03 group file.

If I run read.otu without specifying labels, it dies no matter which group file I use:

mothur > read.otu(list=yagu.stakes.abund.list, group=./yagu.stakes.0.03.abund.groups)
Your group file contains 1322 sequences and list file contains 1275 sequences. Please correct.
For a list of names that are in your group file and not in your list file, please refer to yagu.stakes.abund.missing.name.

mothur > read.otu(list=yagu.stakes.abund.list, group=./yagu.stakes.0.01.abund.groups)

0.01
Error: Sequence 'YaS8.70' was not found in the group file, please correct.

So far, my workaround is to create a separate list files for each label from yagu.stakes.list and run split.abund on each.

2

I am not able to reproduce that. Could you send your files to mothur.bugs@gmail.com so we can track it down?

3

Thanks for bringing this bug to our attention. The way the split.abund command was written, it was creating one list file that was not consistent over the distances since at one distance level a sequence may be part of a rare otu, but at a greater distance it would become part of an abundant otu. The list file should have been written label by label like the group file. The change will be part of version 1.16.0 releasing later this week.