SVDetect : unable to get links.filtered.unique.defined

[tarunmishra.rsg]

Hi all

I am running SVDetect for a matepair data. I am suing the following command line.

SVDetect linking filtering links2bed links2circos links2SV -conf 12L.sv.conf,
My issues are :

1)The program runs fine till the generation of matefile.links.filtered.unique , but while creating the matefile.links.filtered.unique.defined it gives following prompts :

# Defining precise link coordinates...
Use of uninitialized value in hash element at /Apps/serial/SVDetect/SVDetect_r0.5/bin/SVDetect line 782, <LINKS> line 13.
Use of uninitialized value in hash element at /Apps/serial/SVDetect/SVDetect_r0.5/bin/SVDetect line 784, <LINKS> line 13.
Use of uninitialized value in hash element at /Apps/serial/SVDetect/SVDetect_r0.5/bin/SVDetect line 777, <LINKS> line 13.
Use of uninitialized value in hash element at /Apps/serial/SVDetect/SVDetect_r0.5/bin/SVDetect line 778, <LINKS> line 13.
Use of uninitialized value in hash element at /Apps/serial/SVDetect/SVDetect_r0.5/bin/SVDetect line 781, <LINKS> line 13.
Use of uninitialized value in hash element at /Apps/serial/SVDetect/SVDetect_r0.5/bin/SVDetect line 783, <LINKS> line 13.
Can't use an undefined value as an ARRAY reference at /Apps/serial/SVDetect/SVDetect_r0.5/bin/SVDetect line 839, <LINKS> line 13.

It says that for a number of lines and the program stops, beyond this leaving behind matefile.links.filtered.unique.defined of just few kbs(till chr 1 only).

2) I do not get the converted output formats in either of the specified formats(SV,Bed,or circos).

My .conf file has all the parameters same as of the test sample provided with the SVDetect package. My input is a sam file, readlength 50, window size 3000, step size 1500.

Please suggest the possible reason for such a result.

thanks a lot
Tarun

[vedellpt]

could try newer version

It looks like you are using release 0.5. I don`t know if it will help but you could try the most recent release which is perhaps release 0.7f and see if you still get the error.

[Qingl]

Hi,

If you have errors, that means the program doesn't run properly.You may need to check the parameters in your config file. And be careful about the sample names ure text, no underscore for example.
Hope this helps,
Best,
Qing