[InterMine Dev] build failed for fasta

Pengcheng Yang pengchy at gmail.com
Tue Jul 14 08:34:39 BST 2015


Hi,

I have resolved this problem by modify the project.xml to:

Compare to the example in the intermine documentation, I have changed 
the "org.flymine.model.genomic.Chromosome" into 
"org.intermine.model.bio.Chromosome". I don't know why.I can not found 
the org.flymine.model.genomic.Chromosome but found 
malariamine/dbmodel/build/gen/src/org/intermine/model/bio/Chromosome.java, 
I think this is the reason.

Best,
Pengcheng Yang

                 <source name="malaria-chromosome-fasta" type="fasta">
                         <property name="fasta.taxonId" value="36329"/>
                         <property name="fasta.dataSourceName" 
value="PlasmoDB"/>
                         <property name="fasta.dataSetTitle" 
value="PlasmoDB chromosome sequence"/>
                         <property name="fasta.className" 
value="org.intermine.model.bio.Chromosome"/>
                         <property name="fasta.sequenceType" value="dna"/>
                         <property name="fasta.includes" value="MAL*fasta"/>
                         <property name="src.data.dir" 
location="/home/pengchy/Soft/05.SystemBiology/malaria/genome/fasta/"/>
                 </source>

On 2015/7/14 13:26, Pengcheng Yang wrote:
> Hi,
>
> I am building the malariamine example, failed when load genome fasta 
> sequences.
>
> I have successfully run the following command:
>
> # in malariamine/dbmodel
>
> $ /home/pengchy/Soft/09.System/apache-ant-1.9.6/bin/ant clean build-db
>
> ##loading Data
>
> cd ../integrate
>
> $ /home/pengchy/Soft/09.System/apache-ant-1.9.6/bin/ant 
> -Dsource=uniprot-malaria -v
>
> ##loading gff3 data
>
> /home/pengchy/Soft/09.System/apache-ant-1.9.6/bin/ant 
> -Dsource=gff-malaria -v
>
>
> The output of "select class, count(*) from intermineobject group by 
> class;" is listed as [1].
>
>
> But it failed when I load genome fasta data. the project.xml is listed 
> as [2] and the error message is listed as [3].
>
> The message said that "Failed to find any files to process for source: 
> fasta-malaria looked in:
> /home/pengchy/Soft/05.SystemBiology/malaria/genome/fasta". But the 
> fasta files are there.
>
>
> Best,
> Pengcheng Yang
>
> ================================================
> ##attachments
> [1] malariamine=# select class, count(*) from intermineobject group by 
> class;
>                  class                  | count
> ----------------------------------------+-------
>  org.intermine.model.bio.GOTerm         |   665
>  org.intermine.model.bio.Exon           | 13418
>  org.intermine.model.bio.MRNA           |  5556
>  org.intermine.model.bio.GOAnnotation   |  4654
>  org.intermine.model.bio.Ontology       |     2
>  org.intermine.model.bio.GOEvidenceCode |     9
>  org.intermine.model.bio.OntologyTerm   |   193
>  org.intermine.model.bio.Sequence       |  5245
>  org.intermine.model.bio.UniProtFeature |   383
>  org.intermine.model.bio.Protein        |  5245
>  org.intermine.model.bio.Organism       |     1
>  org.intermine.model.bio.CrossReference |  5248
>  org.intermine.model.bio.SOTerm         |     4
>  org.intermine.model.bio.Location       | 24530
>  org.intermine.model.bio.DataSet        |     4
>  org.intermine.model.bio.Synonym        |  6164
>  org.intermine.model.bio.Publication    |   115
>  org.intermine.model.bio.DataSource     |     4
>  org.intermine.model.bio.Gene           |  9034
>  org.intermine.model.bio.Chromosome     |    14
>  org.intermine.model.bio.Comment        |   905
>  org.intermine.model.bio.GOEvidence     |  4654
> (22 rows)
>
>
> [2] /home/pengchy/Soft/05.SystemBiology/intermine/malariamine/project.xml
> <project type="bio">
>   <property name="target.model" value="genomic"/>
>   <property name="source.location" location="../bio/sources/"/>
>   <property name="common.os.prefix" value="common"/>
>   <property name="intermine.properties.file" 
> value="malariamine.properties"/>
>   <property name="default.intermine.properties.file" 
> location="../default.intermine.integrate.properties"/>
>   <sources>
>                 <source name="uniprot-malaria" type="uniprot">
>                         <property name="uniprot.organisms" value="36329"/>
>                         <property name="src.data.dir" 
> location="/home/pengchy/Soft/05.SystemBiology/malaria/uniprot/"/>
>                 </source>
>                 <source name="go-malaria" type="go">
>                         <property name="go.organisms" value="36329"/>
>                         <property name="src.data.dir" 
> location="/home/pengchy/Soft/05.SystemBiology/malaria/go/"/>
>                 </source>
>                 <source name="go-annotation-malaria" type="go-annotation">
>                         <property name="go-annotation.organisms" 
> value="36329"/>
>                         <property name="src.data.dir" 
> location="/home/pengchy/Soft/05.SystemBiology/malaria/go-annotation/"/>
>                 </source>
>                 <source name="fasta-malaria" type="fasta">
>                         <property name="fasta.taxonId" value="36329"/>
>                         <property name="fasta.dataSourceName" 
> value="PlasmoDB"/>
>                         <property name="fasta.dataSetTitle" 
> value="PlasmoDB chromosome sequence"/>
>                         <property name="fasta.className" 
> value="org.flymine.model.genomic.Chromosome"/>
>                         <property name="src.data.dir" 
> location="/home/pengchy/Soft/05.SystemBiology/malaria/genome/fasta/"/>
>                 </source>
>                 <source name="gff-malaria" type="gff">
>                         <property name="gff3.taxonId" value="36329"/>
>                         <property name="gff3.seqClsName" 
> value="Chromosome"/>
>                         <property name="gff3.dataSourceName" 
> value="PlasmoDB"/>
>                         <property name="gff3.seqDataSourceName" 
> value="PlasmoDB"/>
>                         <property name="gff3.dataSetTitle" 
> value="PlasmoDB P.falciparum genome"/>
>                         <property name="src.data.dir" 
> location="/home/pengchy/Soft/05.SystemBiology/malaria/genome/gff/"/>
>                 </source>
>                 <source name="interpro-malaria" type="interpro">
>                         <property name="interpro.organisms" 
> value="36329"/>
>                         <property name="src.data.dir" 
> location="/home/pengchy/Soft/05.SystemBiology/malaria/interpro/"/>
>                 </source>
>                 <source name="kegg-pathway-malaria" type="kegg-pathway">
>                         <property name="kegg-pathway.organisms" 
> value="36329"/>
>                         <property name="src.data.dir" 
> location="/home/pengchy/Soft/05.SystemBiology/malaria/kegg/"/>
>                 </source>
>
>
>   </sources>
>
>   <post-processing>
>
>
>
>   </post-processing>
>
> </project>
>
> [3] the error message of 
> /home/pengchy/Soft/09.System/apache-ant-1.9.6/bin/ant 
> -Dsource=fasta-malaria -v
> Java HotSpot(TM) 64-Bit Server VM warning: ignoring option 
> MaxPermSize=256M; support was removed in 8.0
>
> BUILD FAILED
> /home/pengchy/Soft/05.SystemBiology/intermine/imbuild/integrate.xml:54: The 
> following error occurred while executing this line:
> /home/pengchy/Soft/05.SystemBiology/intermine/bio/sources/fasta/build.xml:44: 
> java.lang.RuntimeException: Failed to find any files to process for 
> source: fasta-malaria looked in:
>         /home/pengchy/Soft/05.SystemBiology/malaria/genome/fasta
>         at 
> org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:68)
>         at 
> org.intermine.bio.dataconversion.FastaLoaderTask.process(FastaLoaderTask.java:163)
>         at 
> org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:132)
>         at 
> org.intermine.bio.dataconversion.FastaLoaderTask.execute(FastaLoaderTask.java:194)
>         at 
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:497)
>         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:435)
>         at org.apache.tools.ant.Target.performTasks(Target.java:456)
>         at 
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
>         at 
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>         at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
>         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
>         at org.intermine.task.Integrate.performAction(Integrate.java:223)
>         at org.intermine.task.Integrate.performAction(Integrate.java:136)
>         at org.intermine.task.Integrate.execute(Integrate.java:127)
>         at 
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:497)
>         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:435)
>         at org.apache.tools.ant.Target.performTasks(Target.java:456)
>         at 
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
>         at org.apache.tools.ant.Project.executeTarget(Project.java:1376)
>         at 
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>         at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
>         at org.apache.tools.ant.Main.runBuild(Main.java:853)
>         at org.apache.tools.ant.Main.startAnt(Main.java:235)
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:285)
>         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:112)
>
> Total time: 18 seconds
>

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