no output with either test data or my own data

[hshcao]

I debugged and it seems to be an samtools problem, everything run fine till samtools kicks in. the test data would go through the whole process. I cannt seem to find the error log. sorry

[JialiUMassWengLab]

It's most likely a samtools version issue. I've remove the dependency on samtools view -X option. Now TEMP works for newer versions of samtools (1.x) as well. Please try again and let me know if it still doesn't work.

Jiali