[maker-devel] Segfault during build_fasta_index

[Fourie Joubert]

Hi Carson

All happy now - much appreciated!

Best regards!

Fourie

On 10/24/2012 05:50 PM, Carson Holt wrote:
> 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.
>>
>


-- 
--------------
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

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