Error retrieving blast results

sequenceserver
#1

Hi,
We have encountered some errors trying to set up sequeceserver 1.0.7.
it seems like blasting works but reporting the results back is not working properly.

Below are the errors.
Any help to solve it would be very much appreciated,
Best regards,
Tomas

Get the following errors:
key “coremake” not found in map source(s).

And (just post the hole thing if it can be helpful to you):

NoMethodError - undefined method root' for nil:NilClass: /state/partition1/home/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sequenceserver-1.0.7/lib/sequenceserver/blast/report.rb:37:in generate’
/state/partition1/home/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sequenceserver-1.0.7/lib/sequenceserver/blast/report.rb:21:in initialize' /state/partition1/home/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sequenceserver-1.0.7/lib/sequenceserver/blast.rb:96:in new’
/state/partition1/home/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sequenceserver-1.0.7/lib/sequenceserver/blast.rb:96:in run' /state/partition1/home/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sequenceserver-1.0.7/lib/sequenceserver/routes.rb:125:in block in class:Routes’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1611:in call' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1611:in block in compile!’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in block (3 levels) in route!' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:994:in route_eval’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in block (2 levels) in route!' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1015:in block in process_route’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in catch' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in process_route’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:973:in block in route!' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in each’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in route!' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1085:in block in dispatch!’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in block in invoke' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in catch’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in invoke' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1082:in dispatch!’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in block in call!' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in block in invoke’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in catch' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in invoke’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in call!' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:895:in call’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/rack-1.6.4/lib/rack/head.rb:13:in call' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:182:in call’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:2013:in call' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in block in call’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1787:in synchronize' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in call’
/state/partition1/home/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/sequenceserver-1.0.7/lib/sequenceserver.rb:92:in call' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/passenger-5.0.25/src/ruby_supportlib/phusion_passenger/rack/thread_handler_extension.rb:97:in process_request’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/passenger-5.0.25/src/ruby_supportlib/phusion_passenger/request_handler/thread_handler.rb:160:in accept_and_process_next_request' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/passenger-5.0.25/src/ruby_supportlib/phusion_passenger/request_handler/thread_handler.rb:113:in main_loop’
/usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/passenger-5.0.25/src/ruby_supportlib/phusion_passenger/request_handler.rb:416:in block (3 levels) in start_threads' /usr/local/packages/ruby-2.3.0/lib/ruby/gems/2.3.0/gems/passenger-5.0.25/src/ruby_supportlib/phusion_passenger/utils.rb:113:in block in create_thread_and_abort_on_exception’

#2

If BLAST worked, I am not sure why the XML should be empty, as is indicated by the stack trace. Running BLAST in the command line will verify this: I would expect to see the ‘key “coremake” not found in map source(s)’ error and no result. I would check two cases. First, without -outfmt option. Secondly with -outfmt 11 and subsequently running blast_formatter -outfmt 5 on the output.

— Priyam

#3

I had encountered the same question.

在 2016年2月28日星期日 UTC+8下午8:24:41，Tomas Larsson写道：

#4

Hi again,
thanks for the quick reply. I finally had time today to go back and try to solve the error.
Turns out it was simply because of a missing/incorrect path to “blast_formatter”.

Now everything works fine!

Best regards,
Tomas