Hi!
I seem to have encountered this bug in the server with the following error message:
NoMethodError - undefined method root' for nil:NilClass: /home/deploy/www/reefgenomics.org/blast_servers/kaust_genomes/lib/sequenceserver/blast/report.rb:37:in generate’ /home/deploy/www/reefgenomics.org/blast_servers/kaust_genomes/lib/sequenceserver/blast/report.rb:21:in initialize' /home/deploy/www/reefgenomics.org/blast_servers/kaust_genomes/lib/sequenceserver/blast.rb:96:in new’ /home/deploy/www/reefgenomics.org/blast_servers/kaust_genomes/lib/sequenceserver/blast.rb:96:in run' /home/deploy/www/reefgenomics.org/blast_servers/kaust_genomes/lib/sequenceserver/routes.rb:110:in block in class:Routes’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1610:in call' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1610:in block in compile!’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in []' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in block (3 levels) in route!’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:993:in route_eval' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in block (2 levels) in route!’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1014:in block in process_route' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in catch’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in process_route' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:972:in block in route!’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in each' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in route!’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1084:in block in dispatch!' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in block in invoke’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in catch' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in invoke’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1081:in dispatch!' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in block in call!’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in block in invoke' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in catch’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in invoke' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in call!’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:894:in call' /usr/lib/ruby/gems/1.9.1/gems/rack-protection-1.5.3/lib/rack/protection/xss_header.rb:18:in call’ /usr/lib/ruby/gems/1.9.1/gems/rack-protection-1.5.3/lib/rack/protection/path_traversal.rb:16:in call' /usr/lib/ruby/gems/1.9.1/gems/rack-protection-1.5.3/lib/rack/protection/json_csrf.rb:18:in call’ /usr/lib/ruby/gems/1.9.1/gems/rack-protection-1.5.3/lib/rack/protection/base.rb:49:in call' /usr/lib/ruby/gems/1.9.1/gems/rack-protection-1.5.3/lib/rack/protection/base.rb:49:in call’ /usr/lib/ruby/gems/1.9.1/gems/rack-protection-1.5.3/lib/rack/protection/frame_options.rb:31:in call' /usr/lib/ruby/gems/1.9.1/gems/rack-1.6.0/lib/rack/head.rb:13:in call’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:181:in call' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:2021:in call’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in block in call' /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1795:in synchronize’ /usr/lib/ruby/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in call' /home/deploy/www/reefgenomics.org/blast_servers/kaust_genomes/lib/sequenceserver.rb:90:in call’ /usr/lib/ruby/gems/1.9.1/gems/passenger-5.0.6/lib/phusion_passenger/rack/thread_handler_extension.rb:85:in process_request' /usr/lib/ruby/gems/1.9.1/gems/passenger-5.0.6/lib/phusion_passenger/request_handler/thread_handler.rb:155:in accept_and_process_next_request’ /usr/lib/ruby/gems/1.9.1/gems/passenger-5.0.6/lib/phusion_passenger/request_handler/thread_handler.rb:110:in main_loop' /usr/lib/ruby/gems/1.9.1/gems/passenger-5.0.6/lib/phusion_passenger/request_handler.rb:414:in block (3 levels) in start_threads’ /usr/lib/ruby/gems/1.9.1/gems/passenger-5.0.6/lib/phusion_passenger/utils.rb:111:in `block in create_thread_and_abort_on_exception’
I wanted to blast a short sequence (primer ) against a genome.
Many thanks in advance for the help,
Hanna