Something went wonky

Niek_Art · February 13, 2017, 2:09am

SequenceServer::BLAST::RuntimeError - Error: NCBI C++ Exception:
    T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_350334_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1481139955/c++/compilers/unix/../../src/corelib/ncbiobj.cpp", line 977: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
     Stack trace:
      blastn ???:0 ncbi::CStackTrace::CStackTrace(std::string const&) offset=0x8B addr=0x1a9587b
      blastn ???:0 ncbi::CException::SetSeverity(ncbi::EDiagSev) offset=0xEB addr=0x1bc0d8b
      blastn ???:0 ncbi::CObject::ThrowNullPointerException() offset=0x2EA addr=0x1c2db5a
      blastn ???:0 ncbi::blast::BlastHitList2SeqAlign_OMF(BlastHitList const*, EBlastProgramType, ncbi::objects::CSeq_loc const&, unsigned int, ncbi::blast::IBlastSeqInfoSrc const*, bool, bool, std::vector<ncbi::TMaskedQueryRegions, std::allocator<ncbi::TMaskedQueryRegions> >&) offset=0xC3C addr=0xdcad5c
      blastn ???:0 blastn() [0xdbf839] offset=0x0 addr=0xdbf839
      blastn ???:0 ncbi::blast::LocalBlastResults2SeqAlign(BlastHSPResults*, ncbi::blast::ILocalQueryData&, ncbi::blast::IBlastSeqInfoSrc const&, EBlastProgramType, bool, bool, std::vector<std::vector<ncbi::TMaskedQueryRegions, std::allocator<ncbi::TMaskedQueryRegions> >, std::allocator<std::vector<ncbi::TMaskedQueryRegions, std::allocator<ncbi::TMaskedQueryRegions> > > >&, ncbi::blast::EResultType) offset=0x8D addr=0xdbf07d
      blastn ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0x378 addr=0xd64e58
      blastn ???:0 ncbi::blast::CLocalBlast::Run() offset=0x3F0 addr=0xd0de00
      blastn ???:0 CBlastnApp::Run() offset=0xDA0 addr=0x986f90
      blastn ???:0 ncbi::CNcbiApplication::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x92A addr=0x1a9ddfa
      blastn ???:0 ncbi::CNcbiApplication::AppMain(int, char const* const*, char const* const*, ncbi::EAppDiagStream, char const*, std::string const&) offset=0x773 addr=0x1a9c653
      blastn ???:0 main offset=0x2CB addr=0x985f3b
      /lib/x86_64-linux-gnu/libc.so.6 ???:0 __libc_start_main offset=0xF5 addr=0x7fe12a34df45
      blastn ???:0 blastn() [0x985b29] offset=0x0 addr=0x985b29

:
/var/lib/gems/1.9.1/gems/sequenceserver-1.0.9/lib/sequenceserver/blast.rb:92:in `run'
/var/lib/gems/1.9.1/gems/sequenceserver-1.0.9/lib/sequenceserver/routes.rb:135:in `block in <class:Routes>'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1611:in `call'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1611:in `block in compile!'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:975:in `[]'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:975:in `block (3 levels) in route!'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:994:in `route_eval'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:975:in `block (2 levels) in route!'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1015:in `block in process_route'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1013:in `catch'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1013:in `process_route'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:973:in `block in route!'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:972:in `each'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:972:in `route!'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1085:in `block in dispatch!'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `block in invoke'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `catch'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `invoke'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1082:in `dispatch!'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:907:in `block in call!'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `block in invoke'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `catch'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `invoke'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:907:in `call!'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:895:in `call'
/var/lib/gems/1.9.1/gems/rack-1.6.5/lib/rack/head.rb:13:in `call'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:182:in `call'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:2013:in `call'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `block in call'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1787:in `synchronize'
/var/lib/gems/1.9.1/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `call'
/var/lib/gems/1.9.1/gems/sequenceserver-1.0.9/lib/sequenceserver.rb:92:in `call'
/var/lib/gems/1.9.1/gems/rack-1.6.5/lib/rack/handler/webrick.rb:88:in `service'
/usr/lib/ruby/1.9.1/webrick/httpserver.rb:138:in `service'
/usr/lib/ruby/1.9.1/webrick/httpserver.rb:94:in `run'
/usr/lib/ruby/1.9.1/webrick/server.rb:191:in `block in start_thread'

Vivek_Rai · February 13, 2017, 5:14am

Hi Niek,

It'd be great if you could provide some additional information:

- Is the error reproducible? What happens if you try different
database and query?
- Query size and database size

Thanks,
Vivek

Niek_Art · February 13, 2017, 8:49am

Hi Vivek,

It works with other databases. I did not see it with nt, nr and a few others.

The one that gave the error was pdbnt. The query was around 25 bases.
Error was reproducible.

I use the latest version of blast+ running in Linux mint rosa.

I'll try it later today again.

Thanks for your fast reply.

Cheers,

Nick

Anurag_Priyam · February 20, 2017, 10:19am

Hi Nick,

There’s a chance your pdbnt download is corrupt. To be sure you will have to verify md5 checksum of each file, or you could try https://github.com/yeban/ncbi-blast-dbs if you don’t mind updating the database along the way.

I read somewhere that the multipart pdbnt requires nt to also be present. Do you know if that is the case? This could be the source of the problem as well. I guess you have nt on your machine. But are they in the same directory? BLAST may also just look for it in the current working directory, which would be a bit of a problem with SequenceServer.

Could you try running BLAST on pdbnt from command line?

Priyam

Niek_Art · February 21, 2017, 8:35pm

Hi Priyam,

I cannot reproduce the error again. I must have changed something...

Oh,

Is it possible to create an output in the form of a taxonomy output like ncbi?

Tax BLAST report

Lineage Report
Organism report
Taxonomy report

Cheers,

Nick

Niek_Art · February 21, 2017, 9:02pm

Hi Priyam,

Error in pdbnt just showed up again.

I deleted the pdbnt database and are using your program to redownload it....

Niek_Art · February 21, 2017, 10:10pm

Hi,

I just downloaded the nt and pdbnt using your software.

The error is still the same.

Which command do you want me to type on the commandline?