[maker-devel] maker 2.22/2.23: Segmentation fault while processing FASTA input
Carson Holt
carsonhh at gmail.com
Mon Mar 26 07:01:52 MDT 2012
Well, if that works, I'd call it a success. Just be careful with any
future updates to BioPerl. Since the root cause of the problem may still
be there.
Thanks,
Carson
On 12-03-26 6:51 AM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:
>Hi,
>
>I was finally able to "fix" the Problem. I tried everything you
>suggested, nice catch on my screwed up Perl lib path btw, but I could
>neither install GDBM_File or NDBM_File nor Berkley_DB separately. In the
>end I simply removed the ISA relations to the modules in question from
>the source code and now it seems to works fine...
>
>sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/'
>
>So thanks a lot for your prompt and comprehensive response, the debug
>executables and the help with the messages.
>
>Regards
>Thomas
>
>
>
>Am 21.03.2012 23:05, schrieb Carson Holt:
>> 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/Inl
>>in
>> 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-la
>>>>>>>>>b.
>>>>>>>>> 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
>>>>>> maker-devel at box290.bluehost.com
>>>>>>
>>>>>>
>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o
>>>>>>rg
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> 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
>>>
>>> _______________________________________________
>>> 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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