CalculateContamination 4.1.2.0 org.apache.commons.math3.exception.TooManyEvaluationsException

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陈星瀚

• October 29, 2021 09:21

a) GATK version used: 4.1.2.0
b) Exact command used: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /products/repos/prod/Akso/BNC/bin/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar CalculateContamination -I conest_oc.tsv -O conest_oc.tsv2 >conest_oc.tsv2.log
c) Entire error log:

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  Pamela Bretscher

  • October 29, 2021 14:55

  Hi 陈星瀚,

  This issue has actually been resolved as of GATK version 4.1.4.1. Could you try upgrading to a newer version of GATK to see if this resolves the error?

  Kind regards,

  Pamela

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