[InterMine Dev] postprocessing speedup?
richard at flymine.org
Wed Mar 28 16:18:11 BST 2012
Sorry we didn't get to this sooner. That doesn't seem right at all,
can you send more of the log from the postprocess directory?
Can you explain a bit more about the situation? How many chromosome
objects do you have loaded? Or have you created each read as a
chromosome feature? What are the feature types loaded?
On 28/03/2012 16:07, Dr. Intikhab Alam wrote:
> Dear Richard/Julie,
> My post-processing (the transfer-sequences) is still running since March
> 18, last write:
> 2012-03-28 18:01:05 INFO org.intermine.bio.postprocess.TransferSequences
> - Starting transfer for AT0200m01A1 chromosome AT0200m01A1.GATTB1C02HV5CP
> 2012-03-28 18:01:05 INFO
> org.intermine.sql.precompute.PrecomputedTableManager - Creating new
> precomputed table CREATE TABLE precomp_1827553
> Is there a way to speedup post-processing e.g. Using multiple processors?
> From: Intikhab Alam <intikhab.alam at kaust.edu.sa
> <mailto:intikhab.alam at kaust.edu.sa>>
> Date: Sat, 24 Mar 2012 17:20:32 +0300
> To: "dev at intermine.org <mailto:dev at intermine.org>" <dev at intermine.org
> <mailto:dev at intermine.org>>
> Subject: [InterMine Dev] postprocessing speedup?
> I am developing a mine for a metagenomic project, containing 4 million
> DNA reads and similar amount of predicted ORFs and related
> attributes/features. Post-processing (transfer-sequences) started
> 2012-03-18 04:38 and still going on.
> Is there a way to paralellize post-processing to speed up these steps
> e.g. On a multiprocessor machine?
> Intikhab Alam, PhD
> Research Scientist
> Computational Bioscience Research Centre (CBRC), Building #2, Office #4336
> 4700 King Abdullah University of Science and Technology (KAUST)
> Thuwal 23955-6900, KSA
> W: http://www.kaust.edu.sa
> T +966 (0) 2 808-2423 F +966 (2) 802 0127
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