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
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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