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Old 02-21-2014, 01:58 AM   #1
mtiwaridros
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Location: germany

Join Date: Feb 2014
Posts: 20
Default Genome generation with STAR

Hi
I want to generate a genome using STAR for subsequent steps.
I got the genome.fa file from UCSC for my organism (dm).
I ran:

Code:
/home/STAR --runMode genomeGenerate --genomeDir /media/star_pipe --genomeFastaFiles genome.fa /media/star_pipe runThread 4
However it has been 15 h now and it is stuck at:
Code:
Starting to generate Genome files
Does it usually take this long or am I doing something wrong?
I have a quad-core CPU with 16 GB RAm, and do not see any unsusal SWAP activity. The CPU usage for STAR is 25-30%.

Any suggestions/corrections will be appreciated.

Thanks.
Manu
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Old 02-21-2014, 03:01 AM   #2
GenoMax
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Posts: 7,091
Default

See this: http://seqanswers.com/forums/showthread.php?t=31815

You may have the runThread option incorrectly specified, should be "--runThreadN 4"

Have you checked to see if the index files are increasing in size?
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Old 02-21-2014, 03:13 AM   #3
mtiwaridros
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Location: germany

Join Date: Feb 2014
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Hi GenoMax

I figured it out.
And its the same as you pointed.

Now I have my built genome file.

Thanks.

Best
Manu
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