STAR running endlessly when mapping a sample

[Ryan Englander]

Hi Dr. Dobin,

I am trying to use STAR to generate splice junctions from an RNA-seq run, but for some reason, one of my samples is running endlessly and times out after running for 3 days. I have successfully mapped this sample in the past, and have used the same commands that are failing here to successfully map other samples (1526/1527 other samples in the cohort).

I have attached the log files, as I am unsure what the problem is. Do you have any idea, or is there any info I can provide to help narrow this problem down?

Thanks so much,

Ryan Englander

[Alexander Dobin]

Hi Ryan,

Which parameters did you map this sample with when it was successful?

I would recommend trying to map this sample without the 2-pass option.