Hi!
I put some jobs and everything (seqtk, trimgalore) seems to work quite fast but bowtie and featureCounts are taking too long to run (more than 10 days have passed). Is there any specific reason for this? Can I do something to avoid this?
Please help.
I am using 44% of my quota. I don’t know if this is a problem.
I am having the exact same issue…
With the same tools (featurecounts and bowtie) or some other tools? How many days have gone by?
I have been trying to run bowtie2 on a collection of 8 subjects (paired end) for about 2 weeks. The first time around I submitted the job with default parameters - one of the subjects finished executing in less than 12 hrs. Three more ran for more than 5 days before I stopped them. On Friday I resubmitted the jobs with the default bowtie2 parameters except that I set the very fast option (–very-fast); none of those jobs have begun execution yet, which is odd compared to my previous experiences. I am at 38% data.
I never re ran my jobs and they’re queued for more than 2 weeks now. I don’t know how to fix the problem. Let me know if you know how to fix the issue or your jobs end up running.