[maker-devel] Segfault during build_fasta_index

[Carson Holt]

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.
>