maker 2.22/2.23: Segmentation fault while processing FASTA input
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maker 2.22/2.23: Segmentation fault while processing FASTA input
 
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Re: maker 2.22/2.23: Segmentation fault while processing FASTA input
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Re: maker 2.22/2.23: Segmentation fault while processing FASTA input
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Re: maker 2.22/2.23: Segmentation fault while processing FASTA input
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Re: maker 2.22/2.23: Segmentation fault while processing FASTA input
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Re: maker 2.22/2.23: Segmentation fault while processing FASTA input
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Re: maker 2.22/2.23: Segmentation fault while processing FASTA input
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In reply to this post by Thomas Hackl
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"<[hidden email]> 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"<[hidden email] >>>>> <mailto:[hidden email]>> 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: [hidden email] >>>>>> <mailto:[hidden email]> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> maker-devel mailing list >>>>>> [hidden email] >>>>>> <mailto:[hidden email]> >>>>>> >>>>>> 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: [hidden email] >>>> <mailto:[hidden email]> >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> [hidden email] >>>> <mailto:[hidden email]> >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> Barry Moore >>> Research Scientist >>> Dept. of Human Genetics >>> University of Utah >>> Salt Lake City, UT 84112 >>> -------------------------------------------- >>> (801) 585-3543 >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> [hidden email] >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> _______________________________________________ >> maker-devel mailing list >> [hidden email] >> 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: [hidden email] _______________________________________________ maker-devel mailing list [hidden email] http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org |
maker_unique.log (133K)
Re: maker 2.22/2.23: Segmentation fault while processing FASTA input
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Re: maker 2.22/2.23: Segmentation fault while processing FASTA input
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Re: maker 2.22/2.23: Segmentation fault while processing FASTA input
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