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@okeefm
Created June 8, 2011 14:37
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Data Source load error
BUILD FAILED
/Users/s-mokeef/code/intermine_0_97/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/s-mokeef/code/intermine_0_97/imbuild/source.xml:253: java.lang.IllegalArgumentException: no class found in model for: Pseudogene (original GFF record type: Pseudogene) for record: <GFF3Record: sequenceID: chr1 source: MGI type: Pseudogene start: 3044314 end: 3044814 score: null strand: + phase: null attributes: {ID=[MGI:3801900], Name=[Gm16088], Note=[pseudogene]}>
at org.intermine.bio.dataconversion.GFF3Converter.process(GFF3Converter.java:173)
at org.intermine.bio.dataconversion.GFF3Converter.parse(GFF3Converter.java:126)
at org.intermine.bio.task.GFF3ConverterTask.execute(GFF3ConverterTask.java:241)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
at sun.reflect.GeneratedMethodAccessor26.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:390)
at org.apache.tools.ant.Target.performTasks(Target.java:411)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
at org.intermine.task.Integrate.performAction(Integrate.java:223)
at org.intermine.task.Integrate.performAction(Integrate.java:135)
at org.intermine.task.Integrate.execute(Integrate.java:127)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
at sun.reflect.GeneratedMethodAccessor26.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:390)
at org.apache.tools.ant.Target.performTasks(Target.java:411)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
at org.apache.tools.ant.Main.runBuild(Main.java:809)
at org.apache.tools.ant.Main.startAnt(Main.java:217)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
chr1 MGI Pseudogene 3044314 3044814 . + . ID=MGI:3801900;Name=Gm16088;Note=pseudogene
chr1 MGI Gene 3195982 3661579 . - . ID=MGI:3528744;Name=Xkr4;Note=protein coding gene
chr1 MGI Gene 3456668 3503634 . + . ID=MGI:3780162;Name=Gm1992;Note=unclassified gene
chr1 MGI Pseudogene 3521876 3522820 . + . ID=MGI:3648497;Name=Gm7341;Note=pseudogene
chr1 MGI Pseudogene 4246316 4251622 . - . ID=MGI:3644986;Name=Gm6101;Note=pseudogene
chr1 MGI Gene 4334224 4350473 . - . ID=MGI:1341105;Name=Rp1;Note=protein coding gene
chr1 MGI Gene 4481009 4486494 . - . ID=MGI:107543;Name=Sox17;Note=protein coding gene
<class name="Gene" extends="SequenceFeature" is-interface="true">
<attribute name="ncbiGeneNumber" type="java.lang.String"/>
<reference name="downstreamIntergenicRegion" referenced-type="IntergenicRegion"/>
<reference name="upstreamIntergenicRegion" referenced-type="IntergenicRegion"/>
<collection name="regulatoryRegions" referenced-type="RegulatoryRegion" reverse-reference="gene"/>
<collection name="proteins" referenced-type="Protein" reverse-reference="genes"/>
<collection name="transcripts" referenced-type="Transcript" reverse-reference="gene"/>
<collection name="goAnnotation" referenced-type="GOAnnotation"/>
<collection name="CDSs" referenced-type="CDS" reverse-reference="gene"/>
<collection name="UTRs" referenced-type="UTR" reverse-reference="gene"/>
<collection name="exons" referenced-type="Exon" reverse-reference="gene"/>
<collection name="flankingRegions" referenced-type="GeneFlankingRegion" reverse-reference="gene"/>
</class>
<class name="Pseudogene" extends="Gene" is-interface="true"></class>
<class name="Gene" extends="SequenceFeature" is-interface="true">
<attribute name="mgiId" type="java.lang.String"/>
<attribute name="ncbiGeneNumber" type="java.lang.String"/>
<attribute name="note" type="java.lang.String"/>
<reference name="downstreamIntergenicRegion" referenced-type="IntergenicRegion"/>
<reference name="upstreamIntergenicRegion" referenced-type="IntergenicRegion"/>
<collection name="regulatoryRegions" referenced-type="RegulatoryRegion" reverse-reference="gene"/>
<collection name="transcripts" referenced-type="Transcript" reverse-reference="gene"/>
<collection name="proteins" referenced-type="Protein" reverse-reference="genes"/>
<collection name="UTRs" referenced-type="UTR" reverse-reference="gene"/>
<collection name="CDSs" referenced-type="CDS" reverse-reference="gene"/>
<collection name="exons" referenced-type="Exon" reverse-reference="gene"/>
<collection name="flankingRegions" referenced-type="GeneFlankingRegion" reverse-reference="gene"/>
<collection name="introns" referenced-type="Intron" reverse-reference="genes"/>
</class>
<?xml version="1.0"?>
<!-- This file details any extensions needed to the data model to store data from this source, everything else is automatically generated from the model description so this is all we need to do to add to the model. -->
<classes>
<class name="Gene" extends="SequenceFeature" is-interface="true">
<attribute name="note" type="java.lang.String" />
<attribute name="mgiId" type="java.lang.String" />
</class>
<class name="Pseudogene" extends="Gene" is-interface="true" />
</classes>
<sources>
<source name="mgi-gtgup" type="mgi-gtgup">
<property name="gff3.seqClsName" value="Chromosome" />
<property name="gff3.seqDataSourceName" value="MGD" />
<property name="gff3.dataSourceName" value="MGD" />
<property name="gff3.dataSetTitle" value="MGI Mouse genome" />
<property name="gff3.taxonId" value="10090" />
<property name="gff3.dontCreateLocations" value="false" />
<property name="src.data.dir" location="/Users/s-mokeef/code/mouse_data/mgi_gtgup/" />
</source>
<source name="update-publications" type="update-publications">
<property name="src.data.file" location="build/publications.xml"/>
</source>
<source name="entrez-organism" type="entrez-organism">
<property name="src.data.file" location="build/organisms.xml"/>
</source>
</sources>
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