error compiling bam_chrom_counter.wdl

David Roe

When I try to compile bam_chrom_counter.wdl from this[1] page, I get this error below. Can anyone help me figure out the problem? This happens for all my wdls and appears to be something that has broke in the last couple days.

1. https://documentation.dnanexus.com/developer/building-and-executing-portable-containers-for-bioinformatics-software/dxcompiler
 

[error] org.fusesource.scalate.TemplateException:

  bad constant pool index: 0 at pos: 49176

     while compiling: <no file>

        during phase: globalPhase=<no phase>, enteringPhase=<some phase>

     library version: version 2.13.7

    compiler version: version 2.13.7

  reconstructed args: -dependencyfile none -deprecation -Wconf:cat=deprecation:w -Wconf:cat=deprecation:ws -Wconf:cat=feature:ws -Wconf:cat=optimizer:ws -classpath /Users/rod1/git/ot2-snake/rod1/dxCompiler-2.11.6.jar -d /var/folders/j1/l1f8thx167z40cry5thjs8wm0000gp/T/scalate-16580645808378117906-workdir/classes

  last tree to typer: EmptyTree

       tree position: <unknown>

            tree tpe: <notype>

              symbol: null

           call site: <none> in <none>

== Source file context for tree position ==

at org.fusesource.scalate.TemplateEngine.compileAndLoad(TemplateEngine.scala:864)

at org.fusesource.scalate.TemplateEngine.compileAndLoadEntry(TemplateEngine.scala:725)

at org.fusesource.scalate.TemplateEngine.liftedTree1$1(TemplateEngine.scala:436)
. . .
at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:561)

at scala.collection.AbstractIterable.foreach(Iterable.scala:926)

at scala.App.main(App.scala:76)

at scala.App.main$(App.scala:74)

at dxCompiler.MainApp$.main(Main.scala:926)

at dxCompiler.MainApp.main(Main.scala)

Caused by: scala.reflect.internal.FatalError:

  bad constant pool index: 0 at pos: 49176

     while compiling: <no file>

        during phase: globalPhase=<no phase>, enteringPhase=<some phase>

     library version: version 2.13.7

    compiler version: version 2.13.7

  reconstructed args: -dependencyfile none -deprecation -Wconf:cat=deprecation:w -Wconf:cat=deprecation:ws -Wconf:cat=feature:ws -Wconf:cat=optimizer:ws -classpath /Users/rod1/git/ot2-snake/rod1/dxCompiler-2.11.6.jar -d /var/folders/j1/l1f8thx167z40cry5thjs8wm0000gp/T/scalate-16580645808378117906-workdir/classes

Comments

6 comments

Date Votes
  • Comment author
    David Roe

    The command is
    java -jar dxCompiler-2.11.6.jar compile bam_chrom_counter.wdl -project <project> -folder /rod1

    0
  • Comment author
    David Roe

    Also happens with dxCompiler-2.11.4.jar

    0
  • Comment author
    David Roe

    It looks like it might be a java issue. I got it to work from a ec2 instance with openjdk 11.0.23.
    Previously, I was using openjdk 22.0.1 from a mac

    0
  • Comment author
    George F The helpers that keep the community running smoothly. UKB Community team Data Analyst

    I think the issue may be related to your java. I can compile successfully on both JupyterLab on RAP and through CLI on Ubuntu on my computer

    0
  • Comment author
    David Roe

    I agree. Thanks for checking.

    0
  • Comment author
    Iman Nazari

    you need to use older version of java version<17

    0

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