[maker-devel] Segfault during build_fasta_index

[Carson Holt]

Glad I could help.

Thanks,
Carson



On 12-10-25 2:51 AM, "Fourie Joubert" <fourie.joubert at up.ac.za> wrote:

>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
>
>-------------------------------------------------------------------------
>This message and attachments are subject to a disclaimer. Please refer
>to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.
>