start up difficulties

sequenceserver
#1

Hi there,
I was recommended to give sequenceserver a try for mining my Trinity.fasta assembly with candidate sequences.
I have formatted the database, but when I call sequenceserver I get the following stuff and there it ends.
I’d appreciate help here.
Thanks:
jahn

kvijed@kvijed-Precision-WorkStation-T7500:~$ sequenceserver

== Initializing SequenceServer…
I, [2014-01-28T11:31:33.944363 #4273] INFO – : Found blastn at /home/kvijed/tools/ncbi-blast-2.2.29+/bin/blastn
I, [2014-01-28T11:31:33.944669 #4273] INFO – : Found blastp at /home/kvijed/tools/ncbi-blast-2.2.29+/bin/blastp
I, [2014-01-28T11:31:33.944767 #4273] INFO – : Found blastx at /home/kvijed/tools/ncbi-blast-2.2.29+/bin/blastx
I, [2014-01-28T11:31:33.944840 #4273] INFO – : Found tblastn at /home/kvijed/tools/ncbi-blast-2.2.29+/bin/tblastn
I, [2014-01-28T11:31:33.944898 #4273] INFO – : Found tblastx at /home/kvijed/tools/ncbi-blast-2.2.29+/bin/tblastx
I, [2014-01-28T11:31:33.944969 #4273] INFO – : Found blastdbcmd at /home/kvijed/tools/ncbi-blast-2.2.29+/bin/blastdbcmd
I, [2014-01-28T11:31:33.945027 #4273] INFO – : Found makeblastdb at /home/kvijed/tools/ncbi-blast-2.2.29+/bin/makeblastdb
I, [2014-01-28T11:31:33.945081 #4273] INFO – : Found blast_formatter at /home/kvijed/tools/ncbi-blast-2.2.29+/bin/blast_formatter
I, [2014-01-28T11:31:33.962483 #4273] INFO – : Found nucleotide database: Sinvicta.cdna at /var/lib/gems/1.9.1/gems/sequenceserver-0.8.7/tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta
I, [2014-01-28T11:31:33.962588 #4273] INFO – : Found protein database: Sinvicta.prot at /var/lib/gems/1.9.1/gems/sequenceserver-0.8.7/tests/database/protein/Sinvicta2-2-3.prot.subset.fasta

I, [2014-01-28T11:31:34.003338 #4273] INFO – : Using WEBrick web server.

== We recommend using Thin web server for better performance.
== To install Thin: [sudo] gem install thin

== Launched SequenceServer at: http://0.0.0.0:4567
== Press CTRL + C to quit.

#2

Hi Jahn,

When you point your browser to http://0.0.0.0:4567 do you see seqserv?

ben

#3

This is the normal startup process. Did you close the terminal window or leave it open? If you start sequence server by calling it in this fashion in the terminal, closing the terminal window will exit the process (just like closing any terminal window will close any process going on it, unless you are using SCREEN or something like that).

If you like, elsewhere on this forum I posted an UPSTART script than can be used to turn sequenceserver into a standard service on Ubuntu so that it will automatically start on boot up and can be controlled like other services - assuming you are using Ubuntu or some other distro that supports UPSTART.