[maker-devel] Segfault during build_fasta_index

[Carson Holt]

Find these lines in these files in MAKER

.../maker/lib/ds_utility.pm:    @AnyDBM_File::ISA = qw(DB_File GDBM_File
NDBM_File SDBM_File);
.../maker/lib/runlog.pm:        @AnyDBM_File::ISA = qw(DB_File GDBM_File
NDBM_File SDBM_File);


And the Bio::DB::Fasta file in BioPerl.  Use this command to identify the
location of Bio::DB::Fasta -->
perl -MBio::DB::Fasta -e 'print $INC{"Bio/DB/Fasta.pm"}."\n"'

.../Bio/DB/Fasta.pm:            @AnyDBM_File::ISA = qw(DB_File GDBM_File
NDBM_File SDBM_File);


Change them all to this -->     @AnyDBM_File::ISA = qw(DB_File);

Use an editor like emacs or vi to make the changes.

Thanks,
Carson



On 12-10-24 11:19 AM, "Fourie Joubert" <fourie.joubert at up.ac.za> wrote:

>Hi Carson
>
>We are indeed running 2.26.
>
>Instructions on editing the statements would be great.
>
>Many thanks for all the help, and sorry for the bother!
>
>Best regards!
>
>Fourie
>
>
>
>
>On 10/24/2012 04:56 PM, Carson Holt wrote:
>> Yes.  I've seen that before.  It's an issue with the @AnyDBM_File::ISA
>> variable. It's set by both BioPerl and a couple of MAKER modules.  If it
>> gets set twice, sometimes you get bugs.
>>
>> Try upgrading to MAKER 2.26 I have a statement in that that will make
>>sure
>> it won't get set wrong.  Otherwise I can give you instructions on
>>editing
>> the BEGIN statements in both BioPerl's Bio::DB::Fasta and the 2 MAKER
>> modules.
>>
>> Thanks,
>> Carson
>>
>>
>> On 12-10-24 10:41 AM, "Fourie Joubert"<fourie.joubert at up.ac.za>  wrote:
>>
>>> Hi
>>>
>>> Really weird - as soon as I add the debug flag - no more segfault...
>>>
>>> Best regards!
>>>
>>> Fourie
>>>
>>>
>>>
>>>
>>> On 10/24/2012 04:33 PM, Carson Holt wrote:
>>>> I'm going to write you a test script that just creates a fasta index
>>>>to
>>>> see if it seg faults.  I'll send it to you later.  For now could you
>>>>run
>>>> maker with the --debug flag set, apture the STDERR and send it to me.
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>> On 12-10-24 10:30 AM, "Fourie Joubert"<fourie.joubert at up.ac.za>
>>>>wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> Darn - did both, but unfortunately still segfaults...
>>>>>
>>>>> Best regards!
>>>>>
>>>>> Fourie
>>>>>
>>>>>
>>>>> On 10/24/2012 04:26 PM, Carson Holt wrote:
>>>>>> Try completely deleting the mpi_blastdb directory under the MAKER
>>>>>> output
>>>>>> folder before restarting.  Perhaps also try reinstalling DB_File via
>>>>>> CPAN.
>>>>>>
>>>>>> --Carson
>>>>>>
>>>>>> On 12-10-24 10:24 AM, "Fourie Joubert"<fourie.joubert at up.ac.za>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi
>>>>>>>
>>>>>>> 1.006901
>>>>>>>
>>>>>>> Regards!
>>>>>>>
>>>>>>> Fourie
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 10/24/2012 04:10 PM, Carson Holt wrote:
>>>>>>>> perl -MBio::Root::Version -e 'print
>>>>>>>> "$Bio::Root::Version::VERSION\n"'
>>>>>>> -- 
>>>>>>> --------------
>>>>>>> Prof Fourie Joubert
>>>>>>> Bioinformatics and Computational Biology Unit
>>>>>>> Department of Biochemistry
>>>>>>> University of Pretoria
>>>>>>> fourie.joubert at up.ac.za
>>>>>>> http://www.bi.up.ac.za
>>>>>>> Tel. +27-12-420-5825
>>>>>>> Fax. +27-12-420-5800
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 
>>>>>>>--------------------------------------------------------------------
>>>>>>>--
>>>>>>> --
>>>>>>> -
>>>>>>> This message and attachments are subject to a disclaimer. Please
>>>>>>> refer
>>>>>>> to www.it.up.ac.za/documentation/governance/disclaimer/ for full
>>>>>>> details.
>>>>>>>
>>>>> -- 
>>>>> --------------
>>>>> Prof Fourie Joubert
>>>>> Bioinformatics and Computational Biology Unit
>>>>> Department of Biochemistry
>>>>> University of Pretoria
>>>>> fourie.joubert at up.ac.za
>>>>> http://www.bi.up.ac.za
>>>>> Tel. +27-12-420-5825
>>>>> Fax. +27-12-420-5800
>>>>>
>>>>>
>>>>> 
>>>>>----------------------------------------------------------------------
>>>>>--
>>>>> -
>>>>> This message and attachments are subject to a disclaimer. Please
>>>>>refer
>>>>> to www.it.up.ac.za/documentation/governance/disclaimer/ for full
>>>>> details.
>>>>>
>>>
>>> -- 
>>> --------------
>>> Prof Fourie Joubert
>>> Bioinformatics and Computational Biology Unit
>>> Department of Biochemistry
>>> University of Pretoria
>>> fourie.joubert at up.ac.za
>>> http://www.bi.up.ac.za
>>> Tel. +27-12-420-5825
>>> Fax. +27-12-420-5800
>>>
>>> 
>>>------------------------------------------------------------------------
>>>-
>>> This message and attachments are subject to a disclaimer. Please refer
>>> to www.it.up.ac.za/documentation/governance/disclaimer/ for full
>>>details.
>>>
>>
>
>
>-- 
>--------------
>Prof Fourie Joubert
>Bioinformatics and Computational Biology Unit
>Department of Biochemistry
>University of Pretoria
>fourie.joubert at up.ac.za
>http://www.bi.up.ac.za
>Tel. +27-12-420-5825
>Fax. +27-12-420-5800
>
>-------------------------------------------------------------------------
>This message and attachments are subject to a disclaimer. Please refer
>to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.
>