[maker-devel] ThrowNullPointerException()

[Marcus Naymik]

Thanks, you're right. I had to recompile blast from src with this flag:
-std=c++0x

On Tue, Mar 14, 2017 at 10:36 AM, Carson Holt <carsonhh at gmail.com> wrote:

> The error itself is coming from BLAST. MAKER does provide the command
> used, so you can try it outside of MAKER. You can submit the files used as
> well as command used to the BLAST developers for them to test with.
>
> MAKER deletes files on failure, but if you edit the …/maker/lib/GI.pm, you
> can stop it from deleting files.
>
> Edit line 58 by setting CLEANUP => 0
>
> Then you should be able to grab whatever files maker used to run blast,
> and copy the blast command used from STDERR.
>
> —Carson
>
>
>
> On Mar 14, 2017, at 11:29 AM, Marcus Naymik <mnaymik at tgen.org> wrote:
>
> I have now tried with multiple versions of blast (2.6 and 2.28 binaries
> and built from source) and get the same error:
>
> setting up GFF3 output and fasta chunks
>
> doing blastn of ESTs
>
> running  blast search.
>
> #--------- command -------------#
>
> Widget::blastn:
>
> /home/mnaymik/TOOLS/ncbi-blast-2.2.28+/bin/blastn -db
> /scratch/mnaymik/maker/tmp/maker_cah
>
> #-------------------------------#
>
> Error: NCBI C++ Exception:
>
>     "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp",
> line 925: Cr
>
>
> Error: NCBI C++ Exception:
>
>     "/home/mnaymik/TOOLS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp",
> line 925: Cr
>
>
> examining contents of the fasta file and run log
>
> ERROR: BLASTN failed
>
> --> rank=87, hostname=pnap-pe7-s09
>
> ERROR: Failed while doing blastn of ESTs
>
> ERROR: Chunk failed at level:0, tier_type:3
>
> FAILED CONTIG:6537645
>
>
> ERROR: BLASTN failed
>
> --> rank=88, hostname=pnap-pe7-s09
>
> ERROR: Failed while doing blastn of ESTs
>
> ERROR: Chunk failed at level:0, tier_type:3
>
> FAILED CONTIG:6537659
>
>
> ERROR: Chunk failed at level:4, tier_type:0
>
> FAILED CONTIG:6537645
>
>
> ERROR: Chunk failed at level:4, tier_type:0
>
> FAILED CONTIG:6537659
>
>
>
> On Thu, Mar 2, 2017 at 1:25 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Try reinstalling blast, or upgrade to a newer version of blast.
>>
>> —Carson
>>
>>
>> On Mar 2, 2017, at 1:05 PM, Marcus Naymik <mnaymik at tgen.org> wrote:
>>
>>
>> I have maker running with MPI and I get this error over and over again
>> for every contig. Any Ideas?
>>
>>
>> MAKER WARNING: All old files will be erased before continuing
>>
>> #---------------------------------------------------------------------
>>
>> Now starting the contig!!
>>
>> SeqID: 5239
>>
>> Length: 1395
>>
>> #---------------------------------------------------------------------
>>
>>
>>
>> Error: NCBI C++ Exception:
>>
>>     "/packages/BUILDS/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp",
>> line 925: Criti
>>
>>
>>
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