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sequenceserver
#1

Hi everyone,

I just installed 'sequenceserver' in a virtual machine - opensuse (jeos). The first Blastp run terminates with the below coppied message.

Any ideas on how to overcome the problem?

Best,
Oliver

NoMethodError - undefined method `root' for nil:NilClass:
/usr/lib64/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver/blast/report.rb:38:in `generate'
/usr/lib64/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver/blast/report.rb:21:in `initialize'
/usr/lib64/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver/blast.rb:96:in `new'
/usr/lib64/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver/blast.rb:96:in `run'
/usr/lib64/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver/routes.rb:135:in `block in <class:Routes>'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1611:in `call'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1611:in `block in compile!'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:975:in `block (3 levels) in route!'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:994:in `route_eval'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:975:in `block (2 levels) in route!'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1015:in `block in process_route'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1013:in `catch'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1013:in `process_route'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:973:in `block in route!'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:972:in `each'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:972:in `route!'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1085:in `block in dispatch!'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `block in invoke'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `catch'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `invoke'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1082:in `dispatch!'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:907:in `block in call!'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `block in invoke'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `catch'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `invoke'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:907:in `call!'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:895:in `call'
/usr/lib64/ruby/gems/2.5.0/gems/rack-1.6.11/lib/rack/head.rb:13:in `call'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:182:in `call'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:2013:in `call'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `block in call'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1787:in `synchronize'
/usr/lib64/ruby/gems/2.5.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `call'
/usr/lib64/ruby/gems/2.5.0/gems/sequenceserver-1.0.11/lib/sequenceserver.rb:92:in `call'
/usr/lib64/ruby/gems/2.5.0/gems/rack-1.6.11/lib/rack/handler/webrick.rb:88:in `service'
/usr/lib64/ruby/2.5.0/webrick/httpserver.rb:140:in `service'
/usr/lib64/ruby/2.5.0/webrick/httpserver.rb:96:in `run'
/usr/lib64/ruby/2.5.0/webrick/server.rb:307:in `block in start_thread'

#2

The error suggests that the BLAST output file it empty. That can happen if the BLAST process crashes instead of finishing (successfully or with error).

Usually, recompiling / downloading the correct BLAST binaries solves the problem.

Priyam

#3

Thank you Priyam,

Your tip pointed in the right direction. The blast binaries were not in the search path of the user running the server.
Ameding $PATH did the trick.

Again, many thanks and best regards,

Oliver