NaN p values

[mRcSchwering]

I have a problem concerning p values in the output table of D3E.
A lot of them are NaN (around 80%).

I run the analysis in this sequence:

D3EMakeContol.py infile infile_ctrl Group1

D3ECmd.py infile infile.out Group1 Group2 -m 1 -t 0 -z 0 -n 0
D3ECmd.py infile_ctrl infile_ctrl.out Group1_1 Group1_2 -m 1 -t 0 -z 0 -n 0

D3EAnalysis.py infile.out infile_ctrl.out outfile 1

I have tried it with t 0 and t 3.

It is a set of around 10 000 genes so I am running the job in parallel.
I do this by splitting the original table big_infile:

D3ESplitData.py big_infile Group1 Group2 ./ 300 1

This will create a few smaller tables which are prefixed Group1_Group2_.
For each of them I run the sequence described above.
Then I merge the resulting outfiles with:

D3EMergeOutput.py ./ final.out Group1 Group2