blastn: Error: NCBI C++ Exception

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blastn: Error: NCBI C++ Exception

Thomas

Hi guys,


another error appeared after we installed NCBI BLAST + to our local Galaxy instance and wanted to test it.

After uploading some testdata to our history we tried to run blastn on it and got the following error:

Fatal error: Matched on Error:

Error: NCBI C++ Exception:

    "/opt/galaxy/galaxy-dist/database/tmp/tmphx2DHp/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.

 

With some testing around we figure out the problem:

 

./blastn -query ~/test.fasta -db nt -task blastn -evalue 0.001 -out ~/out2.txt -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -num_threads 8

Doesn’t work until we replaced the “num_threads 8” like it is written in the original “ncbi_blastn_wrapper.xml” with “num_threads 1”  

Editing the .xml also solved the problem within the galaxy surface.

Now my question is, is there any other workaround without editing the” ncbi_blastn_wrapper.xml”?

Searching in the documentation and the mailing list, I did not find anything about this.

We believe this could be of common interest. It would be great if anybody could comment on this. 


Thanks a lot, Thomas

 


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Re: blastn: Error: NCBI C++ Exception

Björn Grüning
Hi Thomas,

which wrapper did you use, the one from the toolshed or testtoolshed?

Can you have a look at that thread please?
http://dev.list.galaxyproject.org/Blast-Errors-td4659419.html



> Hi guys,
>
>
> another error appeared after we installed NCBI BLAST + to our local
> Galaxy instance and wanted to test it.
>
> After uploading some testdata to our history we tried to run blastn on
> it and got the following error:
>
> Fatal error: Matched on Error:
>
> Error: NCBI C++ Exception:
>
>     "/opt/galaxy/galaxy-dist/database/tmp/tmphx2DHp/ncbi-blast-2.2.26
> +-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical:
> ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL
> pointer.
>
>  
>
> With some testing around we figure out the problem:
>
>  
>
> ./blastn -query ~/test.fasta -db nt -task blastn -evalue 0.001 -out
> ~/out2.txt -outfmt "6 std sallseqid score nident positive gaps ppos
> qframe sframe qseq sseq qlen slen" -num_threads 8
>
> Doesn’t work until we replaced the “num_threads 8” like it is written
> in the original “ncbi_blastn_wrapper.xml” with “num_threads 1”  
>
> Editing the .xml also solved the problem within the galaxy surface.
>
> Now my question is, is there any other workaround without editing the”
> ncbi_blastn_wrapper.xml”?

Not yet, the infrastructure is still missing for such a feature, afaik.
Sorry.

Cheers,
Björn

> Searching in the documentation and the mailing list, I did not find
> anything about this.
>
> We believe this could be of common interest. It would be great if
> anybody could comment on this.  
>
>
> Thanks a lot, Thomas
>
>  
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/



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Re: blastn: Error: NCBI C++ Exception

Gianmauro Cuccuru
In reply to this post by Thomas
On 06/12/2013 04:06 PM, Berner, Thomas wrote:

Hi guys,


another error appeared after we installed NCBI BLAST + to our local Galaxy instance and wanted to test it.

After uploading some testdata to our history we tried to run blastn on it and got the following error:

Fatal error: Matched on Error:

Error: NCBI C++ Exception:

    "/opt/galaxy/galaxy-dist/database/tmp/tmphx2DHp/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.

 

With some testing around we figure out the problem:

 

./blastn -query ~/test.fasta -db nt -task blastn -evalue 0.001 -out ~/out2.txt -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -num_threads 8

Doesn’t work until we replaced the “num_threads 8” like it is written in the original “ncbi_blastn_wrapper.xml” with “num_threads 1”  

Editing the .xml also solved the problem within the galaxy surface.

Now my question is, is there any other workaround without editing the” ncbi_blastn_wrapper.xml”?

You can recompile blast+ enabling multithreading (--with-mt option)
--
Mauro

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Re: blastn: Error: NCBI C++ Exception

Peter Cock
In reply to this post by Thomas
On Wed, Jun 12, 2013 at 3:06 PM, Berner, Thomas
<[hidden email]> wrote:

> Hi guys,
>
>
> another error appeared after we installed NCBI BLAST + to our local Galaxy
> instance and wanted to test it.
>
> After uploading some testdata to our history we tried to run blastn on it
> and got the following error:
>
> Fatal error: Matched on Error:
>
> Error: NCBI C++ Exception:
>
>
> "/opt/galaxy/galaxy-dist/database/tmp/tmphx2DHp/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
> line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to
> access NULL pointer.
>
>
>
> With some testing around we figure out the problem:
>
>
>
> ./blastn -query ~/test.fasta -db nt -task blastn -evalue 0.001 -out
> ~/out2.txt -outfmt "6 std sallseqid score nident positive gaps ppos qframe
> sframe qseq sseq qlen slen" -num_threads 8
>
> Doesn’t work until we replaced the “num_threads 8” like it is written in the
> original “ncbi_blastn_wrapper.xml” with “num_threads 1”
>
> Editing the .xml also solved the problem within the galaxy surface.
>
> Now my question is, is there any other workaround without editing the”
> ncbi_blastn_wrapper.xml”?
>
> Searching in the documentation and the mailing list, I did not find anything
> about this.
>
> We believe this could be of common interest. It would be great if anybody
> could comment on this.

Thanks Gianmauro and Björn for your comments.

There are two issues here, one that we would like to be able to
handle multi-threading better via Galaxy configuration on a
per-tool level, but for now it must often be hard coded or
done via tool-specific environment variables.

Here however, the only reason to change the threads is to
avoid an apparent bug in BLAST itself. The key questions
are how was BLAST installed - if from the tool shed which
one (test of main) and which revision (version).

Thanks,

Peter

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Re: blastn: Error: NCBI C++ Exception

Nicola Soranzo
Il giorno gio, 13/06/2013 alle 18.06 +0100, Peter Cock ha scritto:

> On Thu, Jun 13, 2013 at 6:02 PM, Nicola Soranzo <[hidden email]> wrote:
> >>
> >> There are two issues here, one that we would like to be able to
> >> handle multi-threading better via Galaxy configuration on a
> >> per-tool level, but for now it must often be hard coded or
> >> done via tool-specific environment variables.
> >
> > Regarding the configuration of multi-threading for BLAST+ tools, instead
> > of hardcoding "-num_threads 8" in the XML files, I'd like to do
> > implement something like this:
> >
> > http://toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/rev/cca0838c1597
> >
> > What do you think? Should I prepare a pull request to discuss at
> > GCC2013?
>
> That's a sensible idea, something like $BLASTTHREADS as
> an environment variable?

I was thinking something like BLAST_SITE_OPTIONS='-num_threads 8', which
could also include other parameters (e.g. memory limits) in the future.

> I'd still prefer something built into Galaxy like $THREADS or
> $GALAXYTHREADS or whatever which can be sets with a
> default value and adjusted in the per-tool job runner setup
> (e.g. send BLAST jobs to this cluster queue with 16 threads).
>
> This is definitely a good general topic for the tool authors
> and/or BLAST wrapping BoF sessions at the conference:
> http://wiki.galaxyproject.org/Events/GCC2013/BoF/ToolDevelopers
> http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyBlast
>
> Peter


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Re: blastn: Error: NCBI C++ Exception

Peter Cock
In reply to this post by Peter Cock
Resending as the mailing list was down:

On Thu, Jun 13, 2013 at 6:02 PM, Nicola Soranzo <[hidden email]> wrote:

>>
>> There are two issues here, one that we would like to be able to
>> handle multi-threading better via Galaxy configuration on a
>> per-tool level, but for now it must often be hard coded or
>> done via tool-specific environment variables.
>
> Regarding the configuration of multi-threading for BLAST+ tools, instead
> of hardcoding "-num_threads 8" in the XML files, I'd like to do
> implement something like this:
>
> http://toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/rev/cca0838c1597
>
> What do you think? Should I prepare a pull request to discuss at
> GCC2013?

That's a sensible idea, something like $BLASTTHREADS as
an environment variable?

I'd still prefer something built into Galaxy like $THREADS or
$GALAXYTHREADS or whatever which can be sets with a
default value and adjusted in the per-tool job runner setup
(e.g. send BLAST jobs to this cluster queue with 16 threads).

This is definitely a good general topic for the tool authors
and/or BLAST wrapping BoF sessions at the conference:
http://wiki.galaxyproject.org/Events/GCC2013/BoF/ToolDevelopers
http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyBlast

Peter
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