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How to resolve log4j version clash on SPARK

Hi,
by default SPARK 2 has no support for log4j2. It uses Log4j 1.2.17. When I use GATK 4.0.0 build "as-is" (depends on Log4j2) all jobs on SPARK fail due to version clash. How this is supposed to be solved?

As a workaround I was able:

  • relocate Log4j to different package
  • make sure it is included in the {{-spark}} jar (it is excluded by default)

But I believe there must be better and cleaner way of running current GATK 4.0.0 on SPARK.

Thanks!

Issue · Github
by Sheila

Issue Number
2887
State
open
Last Updated

Answers

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