Hello,
I am trying to view a Chado installation using Apollo. After I have selected
the database to view, Apollo will start to load it but then hang at the 50%
mark.
I have installed GMOD-1.1 with all of the ontologies.
Here is the relevant output in the logs:
INFO : APOLLO_ROOT:
/nfs_exports/apps/gnu-apps/ergatis/software/apollo-1.11.5/Apollo
INFO : OS name: Linux
INFO : OS arch: amd64
INFO : Java version: 1.6.0_15
INFO : reading config file
/nfs_exports/apps/gnu-apps/ergatis/software/apollo-1.11.5/Apollo/conf/apollo.cfg
INFO : using history file /home/ergatis/.apollo/apollo.history
INFO : using backup file /home/ergatis/.apollo/apollo.backup
INFO : this is Apollo Genome Annotation and Curation Tool, version 1.11.5, last
updated Mar 16 2010
INFO : connecting to database pcgp as user postgres at
jdbc:postgresql://ergatisvm:5432
ERROR: SQLException running SELECT cv.cvterm_id, cv.name FROM cvterm cv, cv c
WHERE c.cv_id = cv.cv_id AND c.cvname='sequence'
org.postgresql.util.PSQLException: ERROR: relation "cvterm" does not exist
at
org.postgresql.util.PSQLException.parseServerError(PSQLException.java:139)
I can connect to the database from the command line. I also notice that even
if the database were properly connected, this query will fail in gmod-1.1
because "cvname" does not exist in the cvterm table - it should just be name.
It makes me wonder if that is the actual error but it is being caught by an
exception to the whole query.
Any help will be appreciated. Please let me know if you need anything else
from me.
Thanks!
Jared Becksfort
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