Examples of STAR usage in documentation?
Dear Alex and Shawn,
Our server is slightly busy at the moment (Nicolas Nalpas si pulling all the blanket for himself ), but I'll try asap.
It does make sense that jobs submitted simultaneously can't see the genome being loaded into shared memory (we have a looped script submitting a bunch of STAR jobs all within a few seconds from each other). For the record, we recently submitted 10 jobs in such a loop, and we went over our 256GB RAM + 4GB swap, which slowed the server down.
I support this idea, as we previously also had weird experiences with the outFilter(NminMatch) and (others) parameters which seem to filter on a number of consecutive matches rather than total number of matches for instance. I'd rather have detailed description (or maybe a short and a more detailed) of each option than a doubt which requires additional testing and guessing which impeges on my real project time.
Regarding the original point, example usage would be appreciated too. Maybe users could actually participate to such an effort, as we could rapidly gather a diversity of applications along with the combination of options we succesfully used? If so, we'd need some other place than this thread to share our commands.
Kevin
Dear Alex and Shawn,
Could you please try to run 2-3 jobs (without killing your server ) pausing for 10sec between them, and send me the Log.out outputs for each job.
It does make sense that jobs submitted simultaneously can't see the genome being loaded into shared memory (we have a looped script submitting a bunch of STAR jobs all within a few seconds from each other). For the record, we recently submitted 10 jobs in such a loop, and we went over our 256GB RAM + 4GB swap, which slowed the server down.
I think the documentation should include some examples because the explanation is a little confusing.
Regarding the original point, example usage would be appreciated too. Maybe users could actually participate to such an effort, as we could rapidly gather a diversity of applications along with the combination of options we succesfully used? If so, we'd need some other place than this thread to share our commands.
Kevin
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