crash with pdb nucleotide blastn

SequenceServer::BLAST::RuntimeError - Error: NCBI C++ Exception:
    T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_380670_130.14.18.6_9008__PrepareRelease_Linux64-Centos_1508370803/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=0x1bdaceb
      blastn ???:0 ncbi::CException::x_GetStackTrace() offset=0x22C addr=0x1cf7d3c
      blastn ???:0 ncbi::CException::SetSeverity(ncbi::EDiagSev) offset=0x49 addr=0x1cf2a39
      blastn ???:0 ncbi::CObject::ThrowNullPointerException() offset=0x2EA addr=0x1d6688a
      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=0xdfdc1c
      blastn ???:0 blastn() [0xdf26f9] offset=0x0 addr=0xdf26f9
      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=0xdf1f3d
      blastn ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0x365 addr=0xd9c035
      blastn ???:0 ncbi::blast::CLocalBlast::Run() offset=0x3F0 addr=0xd44920
      blastn ???:0 CBlastnApp::Run() offset=0xDA3 addr=0x9aa7d3
      blastn ???:0 ncbi::CNcbiApplication::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x92A addr=0x1be37ba
      blastn ???:0 ncbi::CNcbiApplication::AppMain(int, char const* const*, char const* const*, ncbi::EAppDiagStream, char const*, std::string const&) offset=0x773 addr=0x1be2013
      blastn ???:0 main offset=0x2CB addr=0x9a977b
      /lib/x86_64-linux-gnu/libc.so.6 ???:0 __libc_start_main offset=0xF0 addr=0x7fc643840830
      blastn ???:0 blastn() [0x9a9369] offset=0x0 addr=0x9a9369

:
/var/lib/gems/2.3.0/gems/sequenceserver-1.0.11/lib/sequenceserver/blast.rb:92:in `run'
/var/lib/gems/2.3.0/gems/sequenceserver-1.0.11/lib/sequenceserver/routes.rb:135:in `block in <class:Routes>'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1611:in `call'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1611:in `block in compile!'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:975:in `block (3 levels) in route!'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:994:in `route_eval'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:975:in `block (2 levels) in route!'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1015:in `block in process_route'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1013:in `catch'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1013:in `process_route'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:973:in `block in route!'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:972:in `each'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:972:in `route!'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1085:in `block in dispatch!'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `block in invoke'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `catch'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `invoke'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1082:in `dispatch!'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:907:in `block in call!'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `block in invoke'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `catch'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `invoke'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:907:in `call!'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:895:in `call'
/var/lib/gems/2.3.0/gems/rack-1.6.8/lib/rack/head.rb:13:in `call'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:182:in `call'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:2013:in `call'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `block in call'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1787:in `synchronize'
/var/lib/gems/2.3.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `call'
/var/lib/gems/2.3.0/gems/sequenceserver-1.0.11/lib/sequenceserver.rb:92:in `call'
/var/lib/gems/2.3.0/gems/rack-1.6.8/lib/rack/handler/webrick.rb:88:in `service'
/usr/lib/ruby/2.3.0/webrick/httpserver.rb:140:in `service'
/usr/lib/ruby/2.3.0/webrick/httpserver.rb:96:in `run'
/usr/lib/ruby/2.3.0/webrick/server.rb:296:in `block in start_thread'

This looks like segmentation fault. I would try to recompile BLAST or use pre-compiled binaries from NCBI.

Priyam