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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy bugs >> GARD Processor http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1228669635 Message started by hannah on Dec 7^th, 2008 at 9:07am

Title: GARD Processor
Post by hannah on Dec 7^th, 2008 at 9:07am

Dear all,

I have run the processor successfully on 7 data files, but my 8th file is giving me trouble. It gets down to KH test and then I get an error and segmentation fault:

KH Testing partition 2
Tree 1 base LRT = 22.2011. p-value = 0.9543
Tree 3 base LRT = 22.2011. p-value = Error:MPI Node:0
Operation MAccess is not defined for 0
Current BL Command:jvec[1][k]=vec2[k]
Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Failing at addr:0x31
/opt/gridengine/default/spool/compute-4-11/job_scripts/51182: line 46: 6009 Segmentation fault (core dumped)

Since I have run the other datasets exactly the same way, with no problems, I guess it is something specific to this dataset?

any insight would be appreciated!
Hannah

Title: Re: GARD Processor
Post by Sergei on Dec 7^th, 2008 at 6:04pm

Dear Hannah,

Can you send me (spond at ucsd dot edu) the offending files (both the alignment and the GARD splits file) - I would like you try to recreate the error.

Also, you don't need to run the processor in an MPI environment.

Cheers,
Sergei

Title: Re: GARD Processor
Post by hannah on Dec 7^th, 2008 at 8:20pm

Sergei,

Thanks for the quick reply. I have just sent the files.

I get the error running in either an MPI environment (linux, using only one processor) or non-MPI (gui on mac).

Thanks again,
Hannah

Title: Re: GARD Processor
Post by Sergei on Dec 8^th, 2008 at 11:23am

Dear Hannah,

There indeed was a bug in the processor module. Please download the attached file and drop it (replacing the original) into TemplateBatchFiles of your HyPhy distribution.

Best,
Sergei

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=GARDProcessor.bf (17 KB | )

Title: Re: GARD Processor
Post by hannah on Dec 8^th, 2008 at 12:36pm

Thanks! It worked.

It's refreshing to have responsive and knowledgeable developers; you are enabling the rest of us to do our science. I will spread the good word about HyPhy and GARD.

-Hannah

Title: Re: GARD Processor
Post by Sergei on Dec 8^th, 2008 at 4:25pm

Dear Hannah,

Thanks for the best feedback a developer can hope for. You made my day:)

Cheers,
Sergei