Update snpEFF? Updating snpEff jar causes scalac to fail...
Posted in Ask the GATK team | Last updated on


Comments (3)

Hi GATK Team,

I have been experimenting with newer versions of snpEff and would like to incorporate a newer version into my local GATK build. However, when I update the jar to the snpeff 3.0 release (by updating the ivy specification and copying the jar in into the proper settings/repository/... directory) I get an internal scalar compiler error:

scala.compile.public:
[mkdir] Created dir: /hpc/users/lindem03/packages/gatk-mssm/dev/build/scala/classes
  [echo] Building Scala...
[scalac] Compiling 87 source files to /hpc/users/lindem03/packages/gatk-mssm/dev/build/scala/classes
[scalac] Compiling 107 source files to /hpc/users/lindem03/packages/gatk-mssm/dev/build/scala/classes
[scalac] Exception in thread "main" java.lang.AssertionError: assertion failed: List(object Byte, object Byte)
[scalac]     at scla.tools.nsc.symtab.Symbols$Symbol.suchThat(Symbols.scala:1056)
[scalac]     at scala.tools.nsc.symtab.Symbols$Symbol.companionModule0(Symbols.scala:1271)
[scalac]     at scala.tools.nsc.symtab.Symbols$Symbol.companionModule(Symbols.scala:1281)
[scalac]     at scala.tools.nsc.symtab.Symbols$Symbol.linkedClassOfClass(Symbols.scala:1302)
[scalac]     at scala.tools.nsc.symtab.Definitions$definitions$.addModuleMethod$1(Definitions.scala:711)
[scalac]     at scala.tools.nsc.symtab.Definitions$definitions$.initValueClasses(Definitions.scala:714)
[scalac]     at scala.tools.nsc.symtab.Definitions$definitions$.init(Definitions.scala:791)
[scalac]     at scala.tools.nsc.Global$Run.<init>(Global.scala:604)
[scalac]     at scala.tools.nsc.Main$.process(Main.scala:105)
[scalac]     at scala.tools.nsc.Main$.main(Main.scala:120)
[scalac]     at scala.tools.nsc.Main.main(Main.scala)

Any thoughts? Do I need to modify the snpEff jar in some way to get it play nicely with GATK? That error is so opaque I am not sure where to start debugging. This is against a "clean" directory (I ran ant clean) with java 1.6.0_30

$ java -version
java version "1.6.0_30"
Java(TM) SE Runtime Environment (build 1.6.0_30-b12)
Java HotSpot(TM) 64-Bit Server VM (build 20.5-b03, mixed mode)

and GATK 1.6-24-gdc14575.


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