job takes too long to finish

[Former user]

Dear ROSE group,

I am running ROSE on a relatively big bam file that is about 3GB and an enhancer file that has roughly 50,000 peaks. I extended the ticker parameter, but it has been running two days and hasn't finished yet...Is this normal? Should I use a more stringent enhancer file (with less number of peaks) to speed it up?

Thank you!

[Brian Abraham]

Hello,

We need more information about the status of all jobs to properly diagnose the issue. ROSE_main kicks off several jobs of ROSE_bamToGFF. ROSE_main will continue to run until either the jobs are finished and the rest of SE calling can happen or it will timeout. Are the outputs from these ROSE_bamToGFF jobs being created? What are the jobs still running? Is ROSE_bamToGFF still running or has it died?

Usually when this problem occurs, ROSE_bamToGFF has failed for one reason or another. Please verify that you have a sorted bam file with a .bai index file. Please verify that your input enhancer file is formatted correctly.

[Brian Abraham]

In working offline with the user, we discovered that the bam file chromosome identifiers did not have "chr" in front of their number, while the GFF file did.