OMA, Error in PropagateFunctionByGroup, invalid arguments in intersect (Mac OS)

Question

[linlinzhao.c]

Hello, my first try on running OMA standalone on just two genomes randomly downloaded from 'OMA--export All/All' get stuck in the error:

   Hierarchical Group computation finished. 
  Found 587 toplevel groups

Propagating function through group 8/601
Error, (in PropagateFunctionByGroup) invalid arguments in intersect

Could anyone direct me to find the problem? Thanks a lot!

[linlinzhao.c]

I did all the same on a Linux machine without any problem. Not sure what happened.

Answer 1

[Adrian Altenhoff]

Hi

I'm one of the developers of OMA standalone. Obviously, this should not happen. About these two runs: did you analyse the same dataset, i.e. the same genomes? what were the two platforms? one linux box, what about the other (failing) platform?

The bug seemed to have occurred during the GO function propagation step which is a rather new feature. If you aren't interested in these predictions, you might as a work-around turn that step off by setting the 'DoGroupFunctionPrediction' paramter to false in the paramters file.

Cheers

[linlinzhao.c]

Hi Adrian, a late thanks for the reply. I almost forgot I put a question on Biostar as the problem not showing up in Linux.

Answer 2

[andreag1987]

Hello, I am having the same issue on Linux (Ubuntu 16.04). I have performed the analysis (4 bacterial genomes) without using the export function "OMA--export All/All" and everything went fine. However I would like to have the GO function prediction, can you help me solving the problem? Thanks a lot!

[Adrian Altenhoff]

OMA does not predict gene functions based on the sequences directly, but rather from annotations from other genomes using the fact that orthologs share often the same gene function. Because of that OMA must be provided with existing gene functions. Currently, no annotations for non-exported genomes are considered for this. but we might consider adding that feature later.