[DAS] Ensembl mouse 8.3 DAS server errors

[Marco Pontoglio]

Hi all,

We have installed a local mirror of Ensembl for the human and mouse genomes.
All seems to work perfectly and we are very happy for this.

However, some troubles were found when displaying our local features with
the local DAS server.

In spite of the fact that the DAS server works perfectly on the human genome
(version 8.30a), on the mouse genome (version 8_3c), on the contrary, we
have big problems. In fact, when we try to display our features (contigview)
we get the following error message:

On the contigview panel:
"error retreiving * mouse feature()"

On the log file of Dazzle server:
2002-10-30 12:21:00 DazzleServerMain: DAS Error
rg.biojava.bio.BioException: Failed to create a feature with a location
[3006935,3006935] outside the sequence: name '1', URN
'http://www.ensembl.org/fpc_contig/1?view=620055' length 1000000
    at org.biojava.bio.seq.ViewSequence.createFeature(ViewSequence.java:221)


Our current settings (file dazzlecfg.xml) are shown below.


We are using DazzleServer/0.96 (20020422; BioJava 1.2) and also tried
DazzleServer/0.97 (20020924; BioJava pre-1.3)

Tomcat4 (4.04-full.2jpp)


We noted that if Dazzle is configured for Mouse 8.3 with a "bridge" pointing
to Human 8.30:
(<string name="dbURL"
value="jdbc:mysql://gene.vironc.pasteur.fr/homo_sapiens_core_8_30a" />)
then the display works only for murine chromosomes having a length shorter
than the corresponding human one.



Thank you in advance for you help


Marco Pontoglio and Serge Garbay

marcop@pasteur.fr
garbay@pasteur.fr


============================================================================
===================================================
<?xml version="1.0" ?>

<!-- Configuration for Mouse mus_musculus_core_8_3c
  -->

<dazzle xmlns="http://www.biojava.org/2000/dazzle">

  <resource id="mouse83_bridge" jclass="ensembl.EnsemblHolder">
    <string name="dbURL"
value="jdbc:mysql://our_local_host.domain.fr/mus_musculus_core_8_3c" />
    <string name="dbUser" value="mysql" />
    <string name="dbPass" value="" />
    <int name="schemaVersion" value="8" />
  </resource>

  <datasource id="mouse83" jclass="ensembl.EnsemblReferenceSource">
    <string name="ensemblHolderID" value="mouse83_bridge" />

    <string name="name" value="Mouse 8_3_c" />
    <string name="description" value="The mouse genome from ensembl" />
    <string name="version" value="8_3_c" />

    <string name="stylesheet" value="ensemblbase-style.xml" />
  </datasource>

 <datasource id="p53MouseDataSource"
jclass="ensembl.EnsemblGenericSeqFeatureSource">
   <string name="ensemblHolderID" value="mouse83_bridge" />
   <string name="name" value="p53 mouse" />
   <string name="description" value="p53 Mouse DAS feature" />
   <string name="version" value="1.00" />
   <string name="mapMaster"
value="http://our_local_host.domain.fr:8180/das_mouse/das/mouse83/" />
   <string name="dbURL"
value="jdbc:mysql://our_local_host.domain.fr/ensembl_generic" />
   <string name="dbUser" value="mysql" />
   <string name="dbPass" value="" />
   <string name="tableName" value="p53_mouse" />
   <string name="stylesheet" value="generic-style.xml" />
 </datasource>

</dazzle>