RNA-SeQC just hang on mac without error messages

[daydream1234]

Hi, i am trying to import my existing RNAseq analysis tools to mac. Everything went well but RNA-SeQC.

RNA-SeQC would just hang after "Running IntronicExpressionReadBlock Walker ...." without throw out an error message.

I use exactly the same genome reference files and bam files on both unix and mac so file format wouldn't be an issue.

I got the same error on both RNA-SeQCv1.1.7 and RNA-SeQCv1.1.8 and also on OSX 10.9 and OSX 10.7

Since I am not getting any error message so it is difficult for me to figure out what could be issue. Anybody has similar experience or any suggestions?

Thanks

[GenoMax]

How much RAM do you have on your Mac? Have you checked the activity monitor when you are running this on your Mac to see if you run out of memory.

[daydream1234]

I have 16G and 32G memory on the two macs that I tried out. The activity Monitor reports that java job used about 300MB memory and 16 threads-- this seems fine to me.

[daydream1234]

Thanks for GenoMax's suggestion. It is a heap size issue: I ran java with 2G memory and it seems fix the problem now.