Ox::ParseError - invalid format, elements overlap at line 16326, column 26 [parse.c:565]
:
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver/blast/report.rb:37:in `parse'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver/blast/report.rb:37:in `generate'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver/blast/report.rb:21:in `initialize'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver/blast.rb:96:in `new'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver/blast.rb:96:in `run'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver/routes.rb:125:in `POST /'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1610:in `call'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1610:in `compile!'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in `[]'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in `route!'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:994:in `route_eval'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in `route!'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1015:in `process_route'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in `catch'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in `process_route'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:973:in `route!'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in `each'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in `route!'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1085:in `dispatch!'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `invoke'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `catch'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `invoke'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1082:in `dispatch!'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in `call!'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `invoke'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `catch'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in `invoke'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in `call!'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:895:in `call'
/Library/Ruby/Gems/1.8/gems/rack-1.6.4/lib/rack/head.rb:13:in `call'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:182:in `call'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:2013:in `call'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in `call'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1787:in `synchronize'
/Library/Ruby/Gems/1.8/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in `call'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver.rb:92:in `call'
/Library/Ruby/Gems/1.8/gems/rack-1.6.4/lib/rack/handler/webrick.rb:88:in `service'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/httpserver.rb:104:in `service'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/httpserver.rb:65:in `run'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/server.rb:173:in `start_thread'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/server.rb:162:in `start'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/server.rb:162:in `start_thread'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/server.rb:95:in `start'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/server.rb:92:in `each'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/server.rb:92:in `start'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/server.rb:23:in `start'
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/webrick/server.rb:82:in `start'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver/server.rb:26:in `start'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver/server.rb:9:in `run'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/lib/sequenceserver.rb:55:in `run'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/bin/sequenceserver:417
/Library/Ruby/Gems/1.8/gems/slop-3.6.0/lib/slop.rb:260:in `call'
/Library/Ruby/Gems/1.8/gems/slop-3.6.0/lib/slop.rb:260:in `parse!'
/Library/Ruby/Gems/1.8/gems/slop-3.6.0/lib/slop.rb:65:in `parse!'
/Library/Ruby/Gems/1.8/gems/sequenceserver-1.0.8/bin/sequenceserver:24
/usr/bin/sequenceserver:19:in `load'
/usr/bin/sequenceserver:19
Hi Rachel,
Thanks for the bug report. It'd be nice if you could include some
additional information like the query you used, the database subset
and NCBI BLAST+ version so that we are able to reproduce this at our
end.
Feel free to add any additional information you may want us to know.
Vivek
Hi Rachel,
This one has come up before - BLAST messes up the XML because sequence id aren’t unique across all databases that were searched (as in, the same >abc in two different FASTA files).
Did you get the error when searching more than one database at once? Can you confirm you don’t get this error when searching just one database?
Priyam