Error not clearly reported properly

[shsdev]

If the command in a toolspec contains an invalid path to a tool (tool is not available at the given path), the hadoop job might still run successfully and report "0 ERROR: null" as result in the part-r- joboutput file. There is no hint to what exactly might be the error.

[codecop]

I faced similar issues and changed ToMaR code accordingly. Which version of ToMaR are you using? Maybe the current one fixes the problem.

[shsdev]

I am using the "filelists" branch because in this version directory inputs and output can be defined in the control-file. But that's actually a good point, I will test this using master.