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

Carson Holt carsonhh at gmail.com
Wed Mar 21 16:05:32 MDT 2012 

That is likely the strangest result I could imagine?  The --debug option
really only cause MAKER to print status messages everywhere and nothing
else, so there must be something else going on between the tests.


One things I did notice from the error log though -->
0.49	Inline	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inline.pm
	UNKNOWN	Inline::denter	/home/s187512/perl/lib/perl5/site_perl/5.12.1/Inlin
e/denter.pm


These are both being loaded from perl 5.12.1 (you are using 5.14.1).  That
can cause issues since I know the first one is executed at the C level and
I wouldn't be surprised if the same is true on the second one.



I also saw this -->
Can't locate package GDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package NDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.
Can't locate package SDBM_File for @AnyDBM_File::ISA at
/storage/tmp/software/perl-5.14.1/lib/5.14.1/x86_64-linux-thread-multi/DB_F
ile.pm line 293.



This appears could be related to Bio::DB::Fasta (which would make sense
with the timing of the seg fault).  This is line 405 in the BEGIN
statement for Bio::DB::Fasta
-->  @AnyDBM_File::ISA = qw(DB_File GDBM_File NDBM_File SDBM_File)

I'm not sure what to do about those?  Are you able to install GDBM_File,
NDBM_File, or SDBM_File by themselves?  They really should just be
optional?  I know I don't have NDBM_File, and I don't get an error.
DB_File is part of the perl distribution, but can be updated via CPAN.
Perhaps that would be good to do.  It may just be that DB_file is broken
and falling back to the other modules doesn¹t work because you don't have
them.  There is also the chance that the issue is really with Berkley_DB.
DB_File accesses Berkley_DB and it wants version 1.x, but will work with
2.x and 3.x.  You may need to even go as far as building a new Berkley_DB.

Well that's enough to try for now.

Thanks,
Carson


On 12-03-20 2:16 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi,
>
>I installed and ran the debug version of maker. Without -debug it
>results in the expected segmentation fault. With -debug it paradoxically
>finishes without the error.
>
>I screened the debug log anyway but could not find anything that helped
>me to localize the problem. I attached a condensed version (sort | uniq)
>of the log.
>Any ideas are appreciated.
>
>Regards
>Thomas
>
>
>
>Am 19.03.2012 17:24, schrieb Carson Holt:
>> Ok.  I finished the special debug version over the weekend.  Run with
>> -debug set as a command line flag.  Capture and return the STDERR on
>> failure.  It will list all modules used, the versions, and when they are
>> called so we can see what happens right before failure.
>>
>> http://yandell-lab.org/research/maker_debug.tgz
>>
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 12-03-14 1:57 AM, "Felix Bemm"<felix.bemm at uni-wuerzburg.de>  wrote:
>>
>>> 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>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com
>>>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>>>>
>>>>>>> 
>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.
>>>>>>>or
>>>>>>> g
>>>>>
>>>>> --
>>>>> 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>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> <mailto:maker-devel at box290.bluehost.com>
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>> Barry Moore
>>>> Research Scientist
>>>> Dept. of Human Genetics
>>>> University of Utah
>>>> Salt Lake City, UT 84112
>>>> --------------------------------------------
>>>> (801) 585-3543
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
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>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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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
>
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