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

[Barry Moore]

You might also try a short perl script outside of MAKER to exercise Bio::DB::Fasta (which I believe is the module MAKER uses for Fasta indexing - correct Carson?).

Something like this should work to force indexing:

use Bio::DB::Fasta;
my $db      = Bio::DB::Fasta->new('/path/to/fasta/files');
my $seq      = $db->seq($seqid, $start, $end);

Point it at your fasta directory or file.

B

On Mar 13, 2012, at 3:41 AM, Thomas Hackl wrote:

> 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
> 
> 
> _______________________________________________
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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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