[InterMine Dev] build failed for fasta

Pengcheng Yang pengchy at gmail.com
Tue Jul 14 06:26:16 BST 2015


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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