split.abund - No data in abund.groups

Hello, (edit: I am using v1.12.2)

After running the command, split.abund(fasta=NZ.fasta, list=NZ.unique.filter.fn.list, cutoff=20, label=0.030, group=NZ.groups), mothur outputted a .abund.groups file with no sequences and a .rare.groups file with all the sequences. But, the FASTA and list files did split correctly, where the .abund files contained ca. 90% of the sequences and the .rare files contained ca. 10% of the sequences. Is this a bug, or am I missing something? Below is a list of the files used and their size, note 0 kb for the .abund.groups file and a size of 329230 kb for the .rare.groups, which is identical in size to the original .groups file.


File Names:File Size NZ.groups:329230 NZ.unique.filter.fn.list:7440175 NZ.0.030.rare.groups:329230 NZ.0.030.abund.groups:0 NZ.0.030.rare.fasta:448338 NZ.0.030.abund.fasta:2847457 NZ.unique.filter.fn.abund.list:247603 NZ.unique.filter.fn.rare.list:38567

As a workaround, I added the ‘groups’ parameter to the split.abund command and the group files were parsed correctly. I then concatenated the individual group files into one groups file and used this groups file with the above .abund.list file to create my much desired .abund.shared file.


Thanks for reporting this bug, and sharing your work around. It will be fixed in 1.13.0.