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ssadedin / ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing
http://ssadedin.github.io/ximmer/
GNU Lesser General Public License v2.1
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ERROR: analysis pipeline did not produce expected analysed target region BED (running through docker) #23

Open xexpanderx opened 5 years ago

xexpanderx commented 5 years ago

This is the error:

java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:109)
    at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:131)
Caused by: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
script15555797947551577614884.groovy: 87: unable to resolve class gngs.BED 
 @ line 87, column 18.
   target_regions = new gngs.BED(target_bed).load()
                    ^

1 error

    at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:310)
    at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:958)
    at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:605)
    at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:554)
    at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:298)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:268)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:254)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:211)
    at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:221)
    at groovy.lang.GroovyClassLoader$parseClass.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at bpipe.Runner.main(Runner.groovy:436)
    ... 6 more

Caught: java.lang.RuntimeException: ERROR: analysis pipeline did not produce expected analysed target region BED: /data/Ximmer/Output/run1/regions.analysable.bed
java.lang.RuntimeException: ERROR: analysis pipeline did not produce expected analysed target region BED: /data/Ximmer/Output/run1/regions.analysable.bed
    at Ximmer.generateReport(Ximmer.groovy:1045)
    at Ximmer$generateReport$5.callCurrent(Unknown Source)
    at Ximmer.run(Ximmer.groovy:202)
    at Ximmer$run.call(Unknown Source)
    at Ximmer.main(Ximmer.groovy:1279)

I run it like this:

docker run -e XIMMER_REF=/genome_fasta/hg19.with.mt.fasta -v /data/ref_genomes/hg19/genome_fasta/:/genome_fasta -v /projects/wp3/nobackup/Workspace/:/data ximmer ximmer -c /data/Ximmer/Config/config.txt -v -o /data/Ximmer/Output -nosim

My config.txt file:

bam_files="/data/CNV/BAM_filter_artifakter2/*.bam"
target_regions="/data/Ximmer/Target_region/regions.bed"
concurrency=20
callers {
    xhmm {}
    exomedepth {}
    conifer {
        conifer_svd_num=5
        conifer_call_threshold=1.3}
    cnmops {}
    codex {}
}
jezkoski commented 5 years ago

Is there a solution for this? I got the same error when trying to run the analysis.

kokyriakidis commented 5 years ago

Me too! The same problem! @ssadedin any thoughts?

zhq90 commented 5 years ago

Me too! Having the same problem! Do you have any solutions on this?@ssadedin