SequenceServer 1.0.14 - ParseError

[Tereza Čalounová]

Hi all,

I have encountered this ParseError using SequenceServer version 1.0.14
It happens when blasting single sequence against two nucleotide databases.

Blasting the same sequence against the databases individually (blasting just against one database) works without any error. 

I appreciate any help concerning this.

Best regards,

Tereza

  Ox::ParseError - invalid format, elements overlap at line 6953, column 26 [parse.c:599] : /var/lib/gems/2.7.0/gems/sequenceserver-1.0.14/lib/sequenceserver/blast/report.rb:36:in `load_file' /var/lib/gems/2.7.0/gems/sequenceserver-1.0.14/lib/sequenceserver/blast/report.rb:36:in `generate' /var/lib/gems/2.7.0/gems/sequenceserver-1.0.14/lib/sequenceserver/blast/report.rb:21:in `initialize' /var/lib/gems/2.7.0/gems/sequenceserver-1.0.14/lib/sequenceserver/blast.rb:96:in `new' /var/lib/gems/2.7.0/gems/sequenceserver-1.0.14/lib/sequenceserver/blast.rb:96:in `run' /var/lib/gems/2.7.0/gems/sequenceserver-1.0.14/lib/sequenceserver/routes.rb:135:in `block in <class:Routes>' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1611:in `call' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1611:in `block in compile!' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:975:in `block (3 levels) in route!' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:994:in `route_eval' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:975:in `block (2 levels) in route!' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1015:in `block in process_route' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1013:in `catch' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1013:in `process_route' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:973:in `block in route!' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:972:in `each' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:972:in `route!' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1085:in `block in dispatch!' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `block in invoke' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `catch' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `invoke' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1082:in `dispatch!' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:907:in `block in call!' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `block in invoke' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `catch' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1067:in `invoke' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:907:in `call!' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:895:in `call' /var/lib/gems/2.7.0/gems/rack-1.6.13/lib/rack/head.rb:13:in `call' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:182:in `call' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:2013:in `call' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `block in call' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1787:in `synchronize' /var/lib/gems/2.7.0/gems/sinatra-1.4.8/lib/sinatra/base.rb:1487:in `call' /var/lib/gems/2.7.0/gems/sequenceserver-1.0.14/lib/sequenceserver.rb:96:in `call' /var/lib/gems/2.7.0/gems/rack-1.6.13/lib/rack/handler/webrick.rb:88:in `service' /usr/lib/ruby/2.7.0/webrick/httpserver.rb:140:in `service' /usr/lib/ruby/2.7.0/webrick/httpserver.rb:96:in `run' /usr/lib/ruby/2.7.0/webrick/server.rb:307:in `block in start_thread'

[Anurag Priyam]

Hi Tereza,

I think we have seen this error before. If I remember correctly, this happens when sequence ids are not unique across the searched databases. Also, I think, it only happens for TBLASTX searches. Used to be a bug in BLAST.

You could try making your sequence ids unique. For example, by prefixing the sequence ids with a few letter corresponding to the sequence file. So scaffold0001 in file my_species.fa becomes my_species_scaffold_00001.

Or you could try updating your BLAST version. I would suggest BLAST+ 2.9.0. You can put the downloaded BLAST binaries in ~/.sequenceserver. Then edit the path to the binaries in ~/.sequenceserver.conf file.

Priyam

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