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Old 03-14-2009, 04:25 PM   #1
mchaisso
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Location: Seattle, WA

Join Date: Apr 2008
Posts: 84
Default euler-sr 1.1 is posted

I silently released euler-sr 1.0 a month ago which has many improvements over the version last mentioned on this site.

After getting some feedback and speeding up some spots, version 1.1 is posted online at the euler portal: http://euler-assembler.ucsd.edu/portal


The updates in this include:

Better integration of multiple clone libraries.
Fast k-mer counting.
Support for multiple cores in error correction (Thanks to Wayne Pfeiffer at the San Diego Supercomputer Center).

There will be a couple of more changes in the next two weeks that will greatly increase the size of genome that may be assembled.

I appreciate all your feedback.

Mark Chaisson
UCSD Bioinformatics
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Old 06-05-2009, 12:49 PM   #2
tshea
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Location: cambridge, ma

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Default

In trying to run on multiple cores I get the error:

bad option: -numJobs

I see that numJobs is not an option but that -numCpu is an option:
usage: Assemble.pl readsFile vertexSize [-ruleFile file] [-minMult m] [-noFixErrors] [-numCpu n]

The README example indicates numJobs:
3.5. Using multiple cores.
Make sure you have compiled for multiple cores using 'gmake parallel'
instead of 'gmake'.
Run
${EUSRC}/assembly/Assemble.pl reads.fa 25 -numJobs 3

Thanks for any insight one might have.
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