genome doesn't always load into memory

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What steps will reproduce the problem?
1. star --genomeDir ./hg19 --genomeLoad LoadAndExit

What is the expected output? What do you see instead?
Expected: a loaded genome.
Often, however, we receive error messages in the 'Log.out' file claiming, 
"Another job is still loading the genome, sleeping for 1 min", which isn't true.

What version of the product are you using? On what operating system?
STAR_2.1.4a_r178  on
Red Hat Enterprise Linux Server release 6.3 (Santiago)
Linux version 2.6.32-279.el6.x86_64 (gcc version 4.4.6 20120305 (Red Hat 
4.4.6-4) (GCC)) 

Original issue reported on code.google.com by jarrin...@gmail.com on 21 Nov 2012 at 2:30

[GoogleCodeExporter]

Hi @jarringly

Sorry for belayed reply, please post your questions at the STAR discussion 
group which I check more regularly.

this might happen if one of previous genome loading jobs did not complete 
loading genome and crashed without a proper exit. In this case, STAR cannot 
decide whether another job is still loading STAR, or it died, so STAR keeps 
sleeping. You would need to use --genomeLoad Remove, and then, again, 
--genomeLoad LoadAndExit

Unfortunately, I do not see a good way to solve this issue. 

Original comment by adobin@gmail.com on 30 Nov 2012 at 8:46

• Changed state: Accepted
• Added labels: Type-Task
• Removed labels: Type-Defect

[GoogleCodeExporter]

Original comment by adobin@gmail.com on 25 Feb 2013 at 8:28

• Changed state: Done