Using PathSeqFilterSpark --ignore-alignment-contigs raises error

[abdohlman]

Bug Report

Affected tool(s) or class(es)

PathSeqPipelineSpark

Affected version(s)

GATK 4.2.2.0

Description

I called PathSeqPipelineSpark as follows:

I confirmed my bam file has a contig "chrEBV" in the bam header:

But unfortunately, for some reason PathSeq is not seeing it: ----

Am I using the --ignore-alignment-contigs parameter incorrectly?