[InterMine Dev] build failed for fasta

Julie Sullivan julie at flymine.org
Tue Jul 14 09:24:09 BST 2015


Thanks for letting us know! Sorry for the bother, I will update the 
document to be the correct value.

On 14/07/15 08:34, Pengcheng Yang wrote:
> 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
>>
>
>
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



More information about the dev mailing list