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Old 05-02-2014, 04:56 AM   #1
mtiwaridros
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Location: germany

Join Date: Feb 2014
Posts: 20
Default STAR Mapping taking too long

Hi

I am using Star v 2.3.0 for mapping.
I have 6 samples, all paired-end.
The genome generation step went without any problem.
But the mapping is taking too long: it has been running since last evening and is stuck at the following:
Code:
May 01 19:21:13 ..... Started STAR run
May 01 19:21:19 ..... Started mapping
The sam file size is increasing, but very incrementally. Similarly for the corresponding logout file.

Any ideas why this might be happening??

Thanks
M
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Old 05-02-2014, 09:26 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

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Run top and check the CPU utilization; there could be a problem. Also, how many cores are you running it on, how much memory is available, what is the size of the input, and what is the size of the reference? And, of course, what was your command line?
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