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Old 07-31-2012, 06:08 AM   #1
maria.b
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Location: Paris

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Default exonerate segmentation fault

Hi ,

I'm using SVMerge to detect SV and CNV variant with different caller.
I have some problem with the script runAssembly.pl. It generate a segmentation fault I don't know why.
The probleme is during the exonerate alignment part uniqly for the inversion variant.
If I well understand in the case of INV variant the second exonerate command line is used, for me it's:

exonerate --querytype dna --targettype dna --gapextend -3 --query Chr1/1/Chr1_4324660_INV/velvet/contigs.fa --bestn 100 --model affine:local --joinrangeext 300 --score 15 --target Chr1/1/Chr1_4324660_INV/ref.fa --dnasubmat /path_to_SVMerge/SVMerge-1.1r32/data/submat.txt --hspfilter 200 --dnahspdropoff 10 --showvulgar FALSE --ryo "%S %pi %ql %C\n" > Chr1/1/Chr1_4324660_INV/velvet/exonerate/Chr1_4324660_INV.exon

the main difference with the other exonerate command line (for insertion/deletion variant) is the use of --dnasubmat parameter. But I never use exonerate so I really don't know how to correct the commande line. I test it without the option but it does not work too. I check the input files, they are not empty.
My version of exonerate is :
exonerate from exonerate version 2.2.0
Using glib version 2.22.5
Built on Apr 20 2012
Does someone have any idea?

Regards

Maria
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Old 03-20-2014, 10:05 AM   #2
aaron.odell
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I am running into a similar issue. Did you ever find a solution for this problem?
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Old 03-20-2014, 11:19 AM   #3
sklages
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You should probably ask the author and post back the solution here ..
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Old 03-20-2014, 01:07 PM   #4
aaron.odell
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Our problem was that we compiled exonerate 2.2.0 from source. Replacing it with the binary version exonerate-2.2.0-x86_64.tar.gz solved the issue.
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