Errno::ENOMEM - Cannot allocate memory:
/usr/lib/ruby/gems/1.8/gems/sequenceserver-1.0.3/lib/sequenceserver/blast.rb:67:in `system'
/usr/lib/ruby/gems/1.8/gems/sequenceserver-1.0.3/lib/sequenceserver/blast.rb:67:in `run'
/usr/lib/ruby/gems/1.8/gems/sequenceserver-1.0.3/lib/sequenceserver/routes.rb:125:in `POST /'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1609:in `call'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1609:in `compile!'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in `[]'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in `route!'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:993:in `route_eval'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:974:in `route!'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1014:in `process_route'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in `catch'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1012:in `process_route'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:972:in `route!'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in `each'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:971:in `route!'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1084:in `dispatch!'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `invoke'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `catch'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `invoke'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1081:in `dispatch!'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in `call!'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `invoke'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `catch'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1066:in `invoke'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:906:in `call!'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:894:in `call'
/usr/lib/ruby/gems/1.8/gems/rack-1.6.1/lib/rack/head.rb:13:in `call'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:181:in `call'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:2021:in `call'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in `call'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1795:in `synchronize'
/usr/lib/ruby/gems/1.8/gems/sinatra-1.4.6/lib/sinatra/base.rb:1486:in `call'
/usr/lib/ruby/gems/1.8/gems/sequenceserver-1.0.3/lib/sequenceserver.rb:90:in `call'
/usr/lib/ruby/gems/1.8/gems/rack-1.6.1/lib/rack/handler/webrick.rb:89:in `service'
/usr/lib/ruby/1.8/webrick/httpserver.rb:104:in `service'
/usr/lib/ruby/1.8/webrick/httpserver.rb:65:in `run'
/usr/lib/ruby/1.8/webrick/server.rb:173:in `start_thread'
/usr/lib/ruby/1.8/webrick/server.rb:162:in `start'
/usr/lib/ruby/1.8/webrick/server.rb:162:in `start_thread'
/usr/lib/ruby/1.8/webrick/server.rb:95:in `start'
/usr/lib/ruby/1.8/webrick/server.rb:92:in `each'
/usr/lib/ruby/1.8/webrick/server.rb:92:in `start'
/usr/lib/ruby/1.8/webrick/server.rb:23:in `start'
/usr/lib/ruby/1.8/webrick/server.rb:82:in `start'
/usr/lib/ruby/gems/1.8/gems/sequenceserver-1.0.3/lib/sequenceserver/server.rb:26:in `start'
/usr/lib/ruby/gems/1.8/gems/sequenceserver-1.0.3/lib/sequenceserver/server.rb:9:in `run'
/usr/lib/ruby/gems/1.8/gems/sequenceserver-1.0.3/lib/sequenceserver.rb:55:in `run'
/usr/lib/ruby/gems/1.8/gems/sequenceserver-1.0.3/bin/sequenceserver:391
/usr/lib/ruby/gems/1.8/gems/slop-3.6.0/lib/slop.rb:260:in `call'
/usr/lib/ruby/gems/1.8/gems/slop-3.6.0/lib/slop.rb:260:in `parse!'
/usr/lib/ruby/gems/1.8/gems/slop-3.6.0/lib/slop.rb:65:in `parse!'
/usr/lib/ruby/gems/1.8/gems/sequenceserver-1.0.3/bin/sequenceserver:12
/usr/bin/sequenceserver:19:in `load'
/usr/bin/sequenceserver:19
I just read an older post with the same message https://groups.google.com/forum/?fromgroups#!topic/sequenceserver/ZRE80eKcBEI
it looks like a memory issue 
cheers
jc
This error message has been posted 2-3 times to the group now, which is a little concerning. I am not sure if and what SequenceServer can do about it. But first I need to understand why are we getting this error:
- How much RAM do you have?
- How many sequences (queries) are you blasting? Is the database huge (like NCBI nr for example)?
- Does it help if you limit the number of hits returned by adding for example “-evalue 1e-3 -max_target_seqs 10” (without the quotes) to the advanced params box?
Priyam
Hi, thanks for answering…
- i have 7.8 GB usable
- i blast only one sequence at a time, searching in the olive genome.
- didn’t help
Hi all,
I am also facing the described problem. This problem started during march and is still present. Interestingly, weeks before (and also months before) I could perform all alignments without any problem. I used the same hardware and even the same BLAST parameters as well as the same sequence. Unfortunately, limiting the number of hits does not help.
Best,
Jascha
Thank you for the info. Can you tell me if this is on Ubuntu / other Linux / Mac and which version of Ruby are you using? Are you able to try with a different (newer) version of Ruby?
Priyam
Sorry, I should have noted that I used the online sequence server (http://denovo.cnag.cat/genomes/olive/blast/#Query_1_hit_1) instead of a local version. Therefore, my hardware and OS should not have any influence, if I am not mistaken?!
Right, no your local hardware can’t be causing this :). I suggest trying to contact admin of that SequenceServer instance and let him/her know of this problem. In the meantime, maybe you can setup SequenceServer locally (they have a downloads page - http://denovo.cnag.cat/genomes/olive/)
Priyam