[maker-devel] maker 2.22/2.23: Segmentation fault while processing FASTA input

[Carson Holt]

There should be no new hardware requirement.  But there is always a chance
that there is an issue with one of the perl modules being used.  I assume
the failure is happening when using maker serially and you are not using
MPI.

Could you reinstall the following perl modules, and try again.  If you are
using CPAN, do a 'force install' to force it to reinstall.

Modules:
*Storable
*Inline::C
*forks
*forks::shared

Also try reinstalling the latest version of BioPerl.

The fact that this is a seg fault suggests that something is happemning at
the C level (just outside of Perl).  Those area all the modules MAKER uses
that will call back to the C level.  BioPerl has a fasta indexing module
that is also making calls outside of Perl, and the fact it fails at that
point makes it a suspect.

Let me know what happens.  I can always generate an alternate MAKER
executable for you to run with additional status messages that may help
identify exactly which module is being called right before the failure.

Thanks,
Carson



On 12-03-07 3:31 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hello,
>
>we want to use a current release of maker (2.22, 2.23) but the program
>terminates with a seg fault while processing the input FASTA files.
>maker 2.15 , which we have been using for quite some time, runs
>perfectly with identical data and setup.
>
>Please contact me if you need specifics on hardware, OS or anything else.
>
>Best regards
>Thomas
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universität
>Department of Bioinformatics
>97074 Würzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
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