Hi,

I am testing OMA version 2.1.1 on a Linux cluster. The program works fine with both the toyexample dataset and my own data. However, setting DoGroupFunctionPrediction := true; in parameter.drw produces an empty gene_function.gaf file (with the exception of the header).

No error message in the std out file, only warnings that taxa cannot be mapped to a clade (below is the corresponding output obtain with the ToyExample:

ReadLibrary: /n/home01/lassance/Software/OMA.2.1.1/OMA/OMA.2.1.1/lib/FunctionPropagation
{--> enter module, args = 
<-- exit module = proc (new_terms, fn:string) local i, genome, tax_id, j, e, id,
a; OpenWriting(fn); printf(!gaf-version: 2.1
); printf(! Functional prediction from OMA standalone using OMA groups.
); for i to NG do DB := DBs[i]; genome := genomes[i]; tax_id := GS[genome,
TAXONID]; if tax_id =  then tax_id := string(-1) fi; for j to GS[genome,
TotEntries] do e := Entry(j); id := sprintf(%s:%05d,genome,j); for a in 
combine_terms(SearchTag(GO,e),new_terms[i,j]) do write_gaf_entry(tax_id,e,id,op(
a)) od od od; OpenWriting(previous) end}
{--> enter PropagateFunctionByGroup, args = [[0, 0, 15, 13], [0, 0, 13, 11], [0,
0, 16, 14], [0, 1, 7, 6], [0, 6, 6, 5], [10, 0, 21, 19], [0, 5, 4, 3], [0, 0, 8,
7], [9, 17, 0, 0], [0, 14, 5, 4], [0, 0, 1, 1], [0, 0, 17, 15], [8, 18, 20, 18],
[0, 0, 9, 8], [0, 8, 11, 9], [0, 0, 12, 10], [0, 2, 2, 2], [0, 0, 18, 16], [0, 0
, 14, 12], [0, 4, 19, 17]], Tree(Leaf(dog,-41.833333,1),0,Tree(Tree(Leaf(mouse2,
-41.282218,4),-41.051115,Leaf(mouse,-41.051115,3),0.33429712),-40.630449,Leaf(
human,-43.166667,2),1))
WARNING: Unable to map dog to a clade. Will not propage function.
WARNING: Unable to map human to a clade. Will not propage function.
WARNING: Unable to map mouse to a clade. Will not propage function.
WARNING: Unable to map mouse2 to a clade. Will not propage function.
dog does not belong to a valid clade.
human does not belong to a valid clade.
mouse does not belong to a valid clade.
mouse2 does not belong to a valid clade.
Propagating function through group 20/20
  Predicted 0 annotations across 20 groups.
  Prediction took 0.00 seconds.
<-- exit PropagateFunctionByGroup = [table([],{}), table([],{}), table([],{}), 
table([],{})]}

If the option is only available with specific datasets it would be good to know. Or am I missing something to get the function prediction to work properly?

Advice/suggestion most welcome!

JML