fasta download error

sequenceserver
#1

Hi there, I’ve been using sequenceserver for quite a bit and it’s great. I recently upgraded and ran into an error. My protein fasta db has * symbols at the end indicating stop codons. It looks like the error is related to unexpected characters in the db, so I wondered if that’s causing the problem. Here’s the error.
Could you take a look please?
Thanks so much,
Simon

ArgumentError - invalid byte sequence in UTF-8:
/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver/sequence.rb:197:in split' /Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver/sequence.rb:197:in block in run’
/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver/sequence.rb:196:in each_line' /Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver/sequence.rb:196:in each’
/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver/sequence.rb:196:in map' /Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver/sequence.rb:196:in run’
/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver/sequence.rb:172:in initialize' /Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver/routes.rb:142:in new’
/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver/routes.rb:142:in block in <class:Routes>' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1611:in call’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1611:in block in compile!' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in []’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in block (3 levels) in route!' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:994:in route_eval’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:975:in block (2 levels) in route!' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1015:in block in process_route’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in catch' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1013:in process_route’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:973:in block in route!' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in each’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:972:in route!' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1085:in block in dispatch!’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in block in invoke' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in catch’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in invoke' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1082:in dispatch!’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in block in call!' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in block in invoke’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in catch' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1067:in invoke’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:907:in call!' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:895:in call’
/Library/Ruby/Gems/2.0.0/gems/rack-1.6.4/lib/rack/head.rb:13:in call' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:182:in call’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:2013:in call' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in block in call’
/Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1787:in synchronize' /Library/Ruby/Gems/2.0.0/gems/sinatra-1.4.7/lib/sinatra/base.rb:1487:in call’
/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.8/lib/sequenceserver.rb:99:in call' /Library/Ruby/Gems/2.0.0/gems/rack-1.6.4/lib/rack/handler/webrick.rb:88:in service’
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/webrick/httpserver.rb:138:in service' /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/webrick/httpserver.rb:94:in run’
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/webrick/server.rb:295:in `block in start_thread’

#2

Hi Simon,

I apologise this issue has been reported earlier as well with some suggested workarounds - https://github.com/wurmlab/sequenceserver/issues/188.

I guess I was partly waiting for BLAST to fix it. But I will look into it now.

Priyam

#3

Thanks so much Priyam, I figured the ‘*’ stop codons could be an issue and removed them from my database with unix tools.
Best wishes
Simon