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STAR speed slowing down during run #27
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Hi, there is a brief description of the genomeLoad options in the last chapter of the manual (see below). I agree that a more detailed description could be useful. Cheers genomeLoad NoSharedMemory |
Thanks for the answer. Your alignment method is really lightning fast, Le 3/10/2015 9:09 PM, alexdobin a écrit :
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Since 2.4.0k, the sorting algorithm has been re-worked and requires much less RAM. Try it with 10GB allocated for sorting: --genomeLoad LoadAndKeep --limitBAMsortRAM 10000000000 |
Thanks a lot, Le 4/21/2015 9:37 PM, alexdobin a écrit :
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Hi, I am trying to run a STAR job, but it is taking an unusually long time. I see the mapping speed declined drastically in time (50M reads paired end unstranded, mouse genome mm10, it has been running for 3 days...). I am using 7 threads on a desktop computer with 32Gb RAM running Xubuntu. Not really a dedicated server, really...
I see in the closed issues that there was a similar case, but the error came from an external memory leak. Here, I launch STAR inside a bash shell script function so there are no 3rd party software causing a leak.
I have been reading the manual for the previous version of STAR (2.3.0.1): there is a paragraph on the genomeLoad parameter usage which is not in the new manual. I was thinking of maybe trying to load the genome in the shared memory and see how it goes, after settting the kernel shmmax and shmall parameters.
I have pasted the log files below. The genome index was built successfully,
Thanks a lot for your help!
Cyril Cros
http://pastebin.com/dfDpt8wR <- Log file
http://pastebin.com/2LzzPCid <- Log progress file
EDIT1: I am running several jobs with genomeLoad=LoadAndKeep and an unsorted BAM output (to avoid reserving shared memory for the BAM sorting). A first job was finished sucessfully in 15min only, all went well. I suggest you add to the new version of the manual the paragraph on the option genomeLoad.
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