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

[Felix Bemm]

Hi,

Thomas and I are colleagues and dealing with the same problem here. I 
wrote some test code that forced the indexing and it work fine. We are 
using most of the bioperl seqio and db modules in combination with other 
tools and don't experience the same problem there at the moment.

Regards
Felix

Am 13.03.2012 22:37, schrieb 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:
>
> useBio::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
>>> <mailto: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
>>>> <mailto:thomas.hackl at uni-wuerzburg.de>
>>>>
>>>>
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>>
>>
>> --
>> Thomas Hackl
>> Julius-Maximilians-Universität
>> Department of Bioinformatics
>> 97074 Würzburg, Germany
>> Fon: +49 931 - 31 86883
>> Mail: thomas.hackl at uni-wuerzburg.de <mailto: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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