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Segment Mean must be finite

esalinasesalinas BroadMember, Broadie

I ran GATK4 AllelicCNV program and get an error message saying "Segment Mean must be finite." (see below)

I look at the input files I give the program and no values were listed as "Inf" or "Infinity" or "-Inf" or anything like that.
All the values I saw (sorting numerically on the column a la "sort -g" ) showed values as low as -8 or so and as high as 8 or so with most values near 0. Because I saw values in the range +/- 8 I'm confused as to the source of the error. I'm not sure if this is a bug or a known issue?


14:59:47.184 INFO  AllelicCNV - Shutting down engine
[June 20, 2017 2:59:47 PM UTC] done. Elapsed time: 0.09 minutes.
java.lang.IllegalArgumentException: Segment Mean must be finite.
        at org.broadinstitute.hellbender.utils.param.ParamUtils.isFinite(
        at org.broadinstitute.hellbender.utils.tsv.TableUtils$1.createRecord(
        at org.broadinstitute.hellbender.utils.tsv.TableReader.fetchNextRecord(
        at org.broadinstitute.hellbender.utils.tsv.TableReader.access$200(
        at org.broadinstitute.hellbender.utils.tsv.TableReader$1.hasNext(
        at java.util.Iterator.forEachRemaining(
        at java.util.Spliterators$IteratorSpliterator.forEachRemaining(
        at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(
        at org.broadinstitute.hellbender.Main.mainEntry(
        at org.broadinstitute.hellbender.Main.main(


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    It might be a bug -- what version are you using?

  • esalinasesalinas BroadMember, Broadie

    @Geraldine_VdAuwera I belive this is the JAR gatk-package-4.alpha.2-1136-gc18e780-SNAPSHOT-local.jar so the committ looks to be "gc18e780"

  • sleeslee Member, Broadie, Dev

    @esalinas The segment means in the .seg file should be non log_2 (this is the output of the GATK CNV tool, as indicated in the javadoc), but the tangent normalized coverages in the tn.tsv should be log_2.

    @shlee Perhaps it's worth making this more explicit in the javadoc.

    Future versions of the CNV pipeline will only deal with raw (integer) read-count coverage and only output non log_2 copy-ratio estimates, which will hopefully prevent such sources of confusion.

    Issue · Github
    by shlee

    Issue Number
    Last Updated
  • esalinasesalinas BroadMember, Broadie
    edited June 2017

    @slee thanks for this info that tells about the expected log-2-space-status. It would seem like any data file with a "Mean" or "Average" column with fractional values, particularly that are negative, I would guess are log2. A file with such values that are non-negative integer or have only zeroes after a decimal point I would guess are non-log-2. I can write a script that transforms a file to take log-2 or do 2^x.

  • shleeshlee CambridgeMember, Broadie, Moderator

    @slee, I've updated the docs.

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