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guanchangge / mosaik-aligner

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Speed of MosaikAligner #97

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1.Using illumina paired end sequence, 100bp in length.
2.This is the commandline I am using:  ./MosaikAligner -in 
/working/Re_runs/Guthrie/read.mkb -ia /data/musRefs/musRefs/totalChr261010.dat 
-j /data/musRefs/musRefs/reference_hs15 -out 
/working/Re_runs/Guthrie/mosaik_output.mka -p 14 -hs 15 -mhp 100 -act 20

3.

What is the expected output? What do you see instead?

The alignment is very slow, e.g. ETA of 2345 days...

What version of the product are you using? On what operating system?

I'm using version 1.1.0021 on a linux machine with 16 CPUs, commandline is 
using 14.

Please provide any additional information below.

I know I am doing something wrong.  What is it?  Please help.

Original issue reported on code.google.com by m.si...@har.mrc.ac.uk on 20 Apr 2011 at 9:27