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?
-eddie
14:59:47.184 INFO AllelicCNV - Shutting down engine
[June 20, 2017 2:59:47 PM UTC] org.broadinstitute.hellbender.tools.exome.AllelicCNV done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=910688256
java.lang.IllegalArgumentException: Segment Mean must be finite.
at org.broadinstitute.hellbender.utils.param.ParamUtils.isFinite(ParamUtils.java:180)
at org.broadinstitute.hellbender.tools.exome.ModeledSegment.<init>(ModeledSegment.java:22)
at org.broadinstitute.hellbender.tools.exome.SegmentUtils.toModeledSegment(SegmentUtils.java:548)
at org.broadinstitute.hellbender.tools.exome.SegmentUtils.lambda$readModeledSegmentsFromSegmentFile$721(SegmentUtils.java:185)
at org.broadinstitute.hellbender.utils.tsv.TableUtils$1.createRecord(TableUtils.java:112)
at org.broadinstitute.hellbender.utils.tsv.TableReader.fetchNextRecord(TableReader.java:355)
at org.broadinstitute.hellbender.utils.tsv.TableReader.access$200(TableReader.java:94)
at org.broadinstitute.hellbender.utils.tsv.TableReader$1.hasNext(TableReader.java:458)
at java.util.Iterator.forEachRemaining(Iterator.java:115)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.exome.SegmentUtils.readSegmentFile(SegmentUtils.java:421)
at org.broadinstitute.hellbender.tools.exome.SegmentUtils.readModeledSegmentsFromSegmentFile(SegmentUtils.java:184)
at org.broadinstitute.hellbender.tools.exome.AllelicCNV.runPipeline(AllelicCNV.java:290)
at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:115)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:170)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:189)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:122)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:143)
at org.broadinstitute.hellbender.Main.main(Main.java:221)
esalinas@eddie-instance-1:~/fc-9c84e685-79f8-4d84-9e52-640943257a9b/ef545f92-5053-4087-ad54-09fa884d0494/wgs_cnv_work/f2df0580-2445-4ea3-af41-d5a8a3107f5b$