Example script stuck at output 19400

[Chao-Yuan Yeh]

I tried to run example.sh on Ubuntu14.04 LTS.

The script seems to be running ok, I checked the process monitor and I can see multiple python process running.

There is a warning message :

In write.table(file = outputFile, superEnhancer, sep = "\t", quote = FALSE, : appending column names to file

Then I see numbers coming up: 200 200 300 ...

It seems to finish a few cycles of "mapping to GFF and making a matrix with fixed bin number" and in some cycles the last number is 19400. Ultimately it reached 19400 and hung.

I see that new files are generated in the example folder, which I cleaned completely before running the example script. I wonder what could have gone wrong?

[Jia Liu]

Hey Chao-Yuan,

Have you solved the problem? I have the same issue, it stop at 21700 and never move on. Could you help me with that please?

Thank you!

[Brian Abraham]

Hi folks, This is not unexpected behavior, depending on what else is still going on. ROSE submits 4x ROSE_bamToGFF.py jobs, each of which create incrementing numbers like you describe. ROSE waits for all 4x to finish, builds enhancer tables, and assigns to genes. Assignment can take many hours to perform, which may be what you're seeing with the "hanging" behavior. If other jobs, including ROSE_geneMapper.py are still running, everything should be working.