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

[Carson Holt]

I've put together a new MAKER executable (mostly finished), and I will get
it to you soon.  This should help focus in on the exact module causing the
issue.

Thanks,
Carson



On 12-03-13 5:41 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> 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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