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Mutect2/GATK4.5 error

I am generating normal vcf files using tumor-only mode with Mutect2/GATK4.5 and bam file after BQSR. I got a error message:

java.lang.IllegalArgumentException: contig must be non-null and not equal to *, and start must be >= 1
at org.broadinstitute.hellbender.utils.clipping.ClippingOp.applyHARDCLIP_BASES(
at org.broadinstitute.hellbender.utils.clipping.ClippingOp.apply(
at org.broadinstitute.hellbender.utils.clipping.ReadClipper.clipRead(
at org.broadinstitute.hellbender.utils.clipping.ReadClipper.clipRead(
at org.broadinstitute.hellbender.utils.clipping.ReadClipper.hardClipSoftClippedBases(
at org.broadinstitute.hellbender.utils.clipping.ReadClipper.hardClipSoftClippedBases(
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(
at org.broadinstitute.hellbender.engine.GATKTool.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(

The re-calibration bam was generated using gatk3.7, without error. Other bams generated the same way did not throw error messages.




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