job takes too long to finish
Issue #24
resolved
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!
Comments (2)
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- changed status to resolved
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.
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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.