I am trying to ues CreatePanelOfNormals
for cnv analysis
java -Xmx4G -jar /ifshk7/BC_PS/luoshizhi/software/gatk/gatk-4.beta.2-4/build/libs/gatk.jar CreatePanelOfNormals -I B.CalculateTargetCoverage/normal_coverage.tsv -O C.CreatePanelOfNormals/ponC.pon --disableSpark
there is only one sample in my normal_coverage.tsv
file.
however,that command exits with this message:
[August 16, 2017 1:03:08 AM HKT] org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=545259520
org.apache.commons.math3.exception.OutOfRangeException: column index (-1)
at org.apache.commons.math3.linear.MatrixUtils.checkColumnIndex(MatrixUtils.java:484)
at org.apache.commons.math3.linear.MatrixUtils.checkSubMatrixIndex(MatrixUtils.java:514)
at org.apache.commons.math3.linear.AbstractRealMatrix.getSubMatrix(AbstractRealMatrix.java:307)
at org.broadinstitute.hellbender.tools.pon.coverage.pca.HDF5PCACoveragePoNCreationUtils.calculateReducedPanelAndPInverses(HDF5PCACoveragePoNCreationUtils.java:312)
at org.broadinstitute.hellbender.tools.pon.coverage.pca.HDF5PCACoveragePoNCreationUtils.create(HDF5PCACoveragePoNCreationUtils.java:106)
at org.broadinstitute.hellbender.tools.exome.CreatePanelOfNormals.runPipeline(CreatePanelOfNormals.java:296)
at org.broadinstitute.hellbender.utils.SparkToggleCommandLineProgram.doWork(SparkToggleCommandLineProgram.java:39)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:116)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:173)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:131)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:152)
at org.broadinstitute.hellbender.Main.main(Main.java:230)
It is a bug?