Error while running OnCOCNV

[Nitin123-4]

Hi I am getting following error while running it:

R.cache v0.12.0 (2015-11-12) successfully loaded. See ?R.cache for help.
Loading required package: lattice
Loading required package: grid
Loading required package: parallel
Error in t.test.default((geneSetout$ratio[tt] - fragRatio)/sdCorrection/geneSet$sd[tt], :
data are essentially constant
Calls: t.test -> t.test.default
In addition: Warning messages:
1: In [<-.factor(*tmp*, i, value = "NA") :
invalid factor level, NA generated
2: In [<-.factor(*tmp*, i, value = "NA") :
invalid factor level, NA generated
Execution halted

Can you please help to resolve the issue.

[valeu]

Dear Nitin,
Can I ask you (1) to run commands from the .sh file one by one to see which R function fails. And also check that all necessary output files were created and are not empty. (2) check that your target file corresponds to the OncoCNV requirements. (3) share with me the input files to the R script that throws the error.
Thank you
Valentina