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.