Problems With Pre-Release Installation

sequenceserver
#1

Hi Folks,

I’m excited to test the new version of SequenceServer! I’ve been using the old version and have been very happy with it. In trying to test the prerelease version, I’ve gone through the automatic setup process on a new server, which works great, except when I get to the database generation. Sequence server appears to successfully generate the database, but then immediately spits the following error message. Any ideas on how to debug?

/home/efishgen/.gem/ruby/1.8/gems/sequenceserver-1.0.0.pre.5/lib/sequenceserver/database.rb:24:in initialize': undefined method downcase!’ for nil:NilClass (NoMethodError)
from /home/efishgen/.gem/ruby/1.8/gems/sequenceserver-1.0.0.pre.5/lib/sequenceserver/database.rb:106:in new' from /home/efishgen/.gem/ruby/1.8/gems/sequenceserver-1.0.0.pre.5/lib/sequenceserver/database.rb:106:in scan_databases_dir’
from /home/efishgen/.gem/ruby/1.8/gems/sequenceserver-1.0.0.pre.5/lib/sequenceserver/database.rb:103:in each_line' from /home/efishgen/.gem/ruby/1.8/gems/sequenceserver-1.0.0.pre.5/lib/sequenceserver/database.rb:103:in scan_databases_dir’
from /home/efishgen/.gem/ruby/1.8/gems/sequenceserver-1.0.0.pre.5/lib/sequenceserver.rb:133:in init_database' from /home/efishgen/.gem/ruby/1.8/gems/sequenceserver-1.0.0.pre.5/lib/sequenceserver.rb:39:in init’
from /home/efishgen/.gem/ruby/1.8/gems/sequenceserver-1.0.0.pre.5/bin/sequenceserver:133
from /home/efishgen/.gem/ruby/1.8/gems/slop-3.6.0/lib/slop.rb:260:in call' from /home/efishgen/.gem/ruby/1.8/gems/slop-3.6.0/lib/slop.rb:260:in parse!’
from /home/efishgen/.gem/ruby/1.8/gems/slop-3.6.0/lib/slop.rb:65:in parse!' from /home/efishgen/.gem/ruby/1.8/gems/sequenceserver-1.0.0.pre.5/bin/sequenceserver:12 from /home/efishgen/.gem/ruby/1.8/bin/sequenceserver:19:in load’
from /home/efishgen/.gem/ruby/1.8/bin/sequenceserver:19

Best,
Jason Gallant

#2

Hi Jason, this looks like the same problem as Malcolm had: you probably have some old databases. Can you check whether there are any “errors” in the output of:

blastdbcmd -recursive -list /n/data1/blast/db -list_outfmt "%f %t %p %n %l %d

(but replace /n/data1/blast/db with your blast db dir?)

#3

Hey Jason,

You could be seeing this error due to incorrect permissions on some database files as well. BLAST+ database files (.nhr, .nin, etc.) should be readable by the user running SequenceServer.

– Priyam

#4

Hi All,

Sorry for the delay— it appears that the problem is with the length (or possibly the content) of the BLAST database “name/description”. Are there certain guidelines as to how long/what characters are allowed in this field?

Best,
Jason

#5

Eh! That’s new. BLAST can be crazy at times.

Sorry, I’m not aware of any guidelines wrt BLAST database title. But I would make the following guess:

  1. Anything other than “a-Z A-Z 0-9 - _ .” would be risky.
  2. Not more than 256 chars. Failing that, not more than 100 chars.

May I ask why is your db title very long or why are using special chars (HTML?). Are you trying to include detailed description about sequences in each database?

– Priyam