split.abund - No data in abund.groups

mothur bugs
1

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.

Charles


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
2

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.


Charles
3

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