RuntimeError - Error: NCBI C++ Exception:

tom.ch...@biogrammatics.com

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Jul 28, 2015, 7:32:34 PM7/28/15

to sequenceserver

Posting error message when blast failed, as requested in error message:

  SequenceServer::BLAST::RuntimeError - Error: NCBI C++ Exception:
    T0 "/Users/coremake/release_build/build/PrepareRelease_IntelMAC_JSID_01_10336_130.14.22.10_9008__PrepareRelease_IntelMAC_1414443170/c++/compilers/unix/../../src/corelib/ncbiobj.cpp", line 926: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.

:
/usr/local/rvm/gems/ruby-2.1.5/gems/sequenceserver-1.0.4/lib/sequenceserver/blast.rb:92:in `run'
/usr/local/rvm/gems/ruby-2.1.5/gems/sequenceserver-1.0.4/lib/sequenceserver/routes.rb:125:in `block in <class:Routes>'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1610:in `call'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1610:in `block in compile!'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in `[]'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in `block (3 levels) in route!'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:993:in `route_eval'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in `block (2 levels) in route!'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1014:in `block in process_route'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in `catch'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in `process_route'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:972:in `block in route!'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in `each'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in `route!'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1084:in `block in dispatch!'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `block in invoke'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `catch'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `invoke'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1081:in `dispatch!'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in `block in call!'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `block in invoke'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `catch'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `invoke'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in `call!'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:894:in `call'
/usr/local/rvm/gems/ruby-2.1.5/gems/rack-1.5.2/lib/rack/head.rb:11:in `call'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:181:in `call'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:2021:in `call'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in `block in call'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1795:in `synchronize'
/usr/local/rvm/gems/ruby-2.1.5/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in `call'
/usr/local/rvm/gems/ruby-2.1.5/gems/sequenceserver-1.0.4/lib/sequenceserver.rb:90:in `call'
/usr/local/rvm/gems/ruby-2.1.5/gems/rack-1.5.2/lib/rack/handler/webrick.rb:60:in `service'
/usr/local/rvm/rubies/ruby-2.1.5/lib/ruby/2.1.0/webrick/httpserver.rb:138:in `service'
/usr/local/rvm/rubies/ruby-2.1.5/lib/ruby/2.1.0/webrick/httpserver.rb:94:in `run'
/usr/local/rvm/rubies/ruby-2.1.5/lib/ruby/2.1.0/webrick/server.rb:295:in `block in start_thread'

Guangtu Gao

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Jul 30, 2015, 11:52:55 AM7/30/15

to sequenceserver, tom.ch...@biogrammatics.com

I got the same error message as I used the current version of sequenceserver. I used the older versions (lower than 1.0) before and I had no issues.
Thanks,
Guangtu

sequenceserver_error.txt

Anurag Priyam

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Jul 31, 2015, 12:12:21 AM7/31/15

to sequenceserver, tom.ch...@biogrammatics.com

It's a problem with your BLAST executable really. Are you compiling the BLAST+ binaries yourself? Using pre-compiled binaries from NCBI should help. If you are using pre-compiled binaries from NCBI then this problem must be reported to NCBI. If you are using packaged BLAST from Debian/RedHat/homewbrew (Mac), please report to the corresponding issue tracker.

-- Priyam

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