Error (NoMethodError from a nil:nilClass) upon BlastP

sequenceserver
#1

Good day,

I was trying to blast a protein sequence using BlastP against the PHI-base 4.1 protein sequences database when the following error occurred during the processing/BLAST-ing stage:

NoMethodError - undefined method exitstatus' for nil:NilClass: /var/lib/gems/1.9.1/gems/sequenceserver-1.0.5/lib/sequenceserver/blast.rb:70:in run’
/var/lib/gems/1.9.1/gems/sequenceserver-1.0.5/lib/sequenceserver/routes.rb:125:in block in <class:Routes>' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1610:in call’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1610:in block in compile!' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in []’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in block (3 levels) in route!' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:993:in route_eval’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in block (2 levels) in route!' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1014:in block in process_route’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in catch' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in process_route’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:972:in block in route!' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in each’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in route!' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1084:in block in dispatch!’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in block in invoke' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in catch’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in invoke' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1081:in dispatch!’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in block in call!' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in block in invoke’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in catch' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in invoke’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in call!' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:894:in call’
/var/lib/gems/1.9.1/gems/rack-1.6.4/lib/rack/head.rb:13:in call' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:181:in call’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:2021:in call' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in block in call’
/var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1795:in synchronize' /var/lib/gems/1.9.1/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in call’
/var/lib/gems/1.9.1/gems/sequenceserver-1.0.5/lib/sequenceserver.rb:90:in call' /var/lib/gems/1.9.1/gems/rack-1.6.4/lib/rack/handler/webrick.rb:88:in service’
/usr/lib/ruby/1.9.1/webrick/httpserver.rb:138:in service' /usr/lib/ruby/1.9.1/webrick/httpserver.rb:94:in run’
/usr/lib/ruby/1.9.1/webrick/server.rb:191:in `block in start_thread’

#2

Just to expand on this:

I was using the online BlastP at PHI-base (http://phi-blast.phi-base.org/)

The sequence I was using was:

>gi>629668491|ref|XP_007796197.1| putative candidate effector 5 protein [Eutypa lata UCREL1]
MFSSKLSIALFGLLGLAAAVPAANLQAETVARSDESHLVARGPDCNNLASGLTLEDCEHISSIGMANQGI
NPTSNNGLIWIGNDGDYTFTFTNGASNNVPVTVVIWNFPAGDYEASFMNVRQPQISYSLPTANTSVTISI
ARDISGGFASLQGHATTLSQWGQIYNTWGEFTTGDWATIDVSRLVNMSGNDMEITVRDNGCVSNMDQCSF
WCKNNLNECGDSGTYDLVNCDNGSQPGATYGSYDGVNPDGGCQGWGANGHVDVVLRD
#3

Do you run phi-blast server? Did you make changes to the code (in blast.rb)? Have you replaced blast binary with a shell script that tries to do more?

Priyam

#4

No, I ran the sequence through yesterday using the BLAST page linked earlier with the lone sequence I mentioned with no additional parameters.

The issue appears to have been resolved though.