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

[Thomas Hackl]

Hello,

We reinstalled the packages you suggested

forks is up to date (0.34).
forks::shared is up to date (0.34).
Inline::C is up to date (0.50).
Storable is up to date (2.30).

as well as BioPerl.

The problem is still the same.

With MPI it terminates with this message:

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
===================================================================================== 


=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================== 

APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

which I presume is also the same problem.

I am with you that the error is caused somewhere on the C level. If the 
indexing step
is handled by non-maker modules exclusively, than the fact that the 2.15 
version works,
suggests that you are using different modules/methods in the current 
releases?

In any case, I think a version with verbose status messages might help 
to localize the
source of the problem.

Regards
Thomas

Am 07.03.2012 23:45, schrieb 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
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


-- 
Thomas Hackl
Julius-Maximilians-Universität
Department of Bioinformatics
97074 Würzburg, Germany
Fon:  +49 931 - 31 86883
Mail: thomas.hackl at uni-wuerzburg.de