Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Building GATK 3.7 and a stackoverflow building Queue Extensions

hemphemp Raleigh, NCMember
edited February 2017 in Ask the GATK team

Occasionally when my CI docker image build runs mvn verify, it gets a stack-overflow error when building GATK Queue Extensions Distribution. This is not 100% of the time and hard to reproduce...sorry for the lack of information. I've tried to capture as much as I could and wondered if anyone else has encountered this in their CI? Increasing the stack size -Xss via MAVEN_OPTS does not help.

Docker information (FROM openjdk:8):

[email protected]:/opt/gatk# git describe --tags
3.7
[email protected]:/opt/gatk# cat /etc/debian_version
8.7
[email protected]:/opt/gatk# java -version
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)
[email protected]:/opt/gatk#

I've attached the full log file. But here is a snippet from it:

...
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.silent(Typers.scala:728)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.normalTypedApply$1(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedApply$1(Typers.scala:4621)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed1(Typers.scala:5526)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.typed1(Erasure.scala:840)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed(Typers.scala:5604)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedQualifier(Typers.scala:5689)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedQualifier(Typers.scala:5697)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.adaptMember(Erasure.scala:786)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.typed1(Erasure.scala:840)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed(Typers.scala:5604)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer$$anonfun$92.apply(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer$$anonfun$92.apply(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.silent(Typers.scala:728)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.normalTypedApply$1(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedApply$1(Typers.scala:4621)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed1(Typers.scala:5526)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.typed1(Erasure.scala:840)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed(Typers.scala:5604)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedQualifier(Typers.scala:5689)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typedQualifier(Typers.scala:5697)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.adaptMember(Erasure.scala:786)
[INFO]  at scala.tools.nsc.transform.Erasure$Eraser.typed1(Erasure.scala:840)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.typed(Typers.scala:5604)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer$$anonfun$92.apply(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer$$anonfun$92.apply(Typers.scala:4570)
[INFO]  at scala.tools.nsc.typechecker.Typers$Typer.silent(Typers.scala:728)
...
Tagged:

Comments

Sign In or Register to comment.