SOAPsv

[Esther Aguilar Master]

Hi forum,

I am testing the SOAPsv method and I am experiencing some troubles in the validation step.

More precisely, I cannot find the correct params to execute scafcomplex805, and I think this is the reason why the program sv_validate_combinator ends with a SegmentationFault.

In the documentation the validation step is as follows:

at prj_sv_renal

mkdir sv

cd sv

ln ../process/human_in* .

awk '{print $1,$3,$4}' max_intro_indels > max_intro_indels.scaflist

nohup scrPATH/scafcomplex805 /FULLPATH/../asm/human.scafSeq.fastat human_intro_indels.scaflist /FULLPATH/../asm/readonscaf/ >scresult 2>scerror &

Which directory should I put in the third parameter?  I put the 'asm' directory, but, if I put a non existing dir, the result is the same.

Could you explain a little bit what is the scafcomplex805 doing? I am very confused.

And as for sv_validate_combinator, I am confused with the first and forth param (the result of scafcomplex805). In the documentation:

scrPATH/sv_validate_combinator human_intro_indels insertion.validated deletion.validated scresult 0 all.validated

I am putting as the first param 'max_intro_indels.scaflist' and I get this:

>sv_validate_combinator ../sv/intro_indels.long insertion.validated deletion.validated ../sv/scresult 0 all.validated

SV validation combinator

Version 0.2

Author: Aqua Lo

Importing SV list...

End Inporting SV list, 131 terms imported, 0s elapsed!

DataBase size: 75

Importing S/P ratio validated list...

End Importing S/P ratio validated list, 16 imported. 0s elapsed!

DataBase size: 75

Importing S/P ratio validated list...

End Importing S/P ratio validated list, 93 imported. 0s elapsed!

DataBase size: 75

Importing scaffolding complexity list...

End Importing scaffolding complexity list, 0 terms imported, 0s elapsed!

DataBase size: 75

Analyzing scaffolding complexity...

  Percentage        Acc.     Entropy      Energy    Contrast   LocalCalm

Segmentation fault

Which I think it is related with the previous command.

Thank you very much.

Esther