I am trying to test my GATK python-based wrapper module, and I have call to CrosscheckFingerprints that should be in the NO-VALID-CHECKS situation (i.e. should raise the exit code passed into the EXIT_CODE_WHEN_MISMATCH parameter.  Instead, I receive an error code of 4 everytime.

a) GATK version used

4.1.7.0

b) Exact GATK commands used

gatk --java-options -Djava.io.tmpdir=/tmp/tmpnd5Qqi -XX:ConcGCThreads=2 -XX:ParallelGCThreads=2 -Xmx4G CrosscheckFingerprints -H hapmap_ccfp_match.vcf.gz -I crosscheck_fingerprints1.bam -O /tmp/tmpWfibWc/output.vcf.gz --CROSSCHECK_MODE CHECK_ALL_OTHERS -SI crosscheck_fingerprints2.bam --EXIT_CODE_WHEN_MISMATCH 0 --EXIT_CODE_WHEN_NO_VALID_CHECKS -42

c) The entire error log if applicable.

[2020-07-22 17:20:55,658] safe_subprocess.py [ERROR] > Jul 22, 2020 5:20:55 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
[2020-07-22 17:20:55,658] safe_subprocess.py [ERROR] > INFO: Failed to detect whether we are running on Google Compute Engine.
[2020-07-22 17:20:55,659] safe_subprocess.py [ERROR] > [Wed Jul 22 17:20:55 UTC 2020] Executing as root@b4e66cfca116 on Linux 4.19.76-linuxkit amd64; OpenJDK 64-Bit Server VM 1.8.0_191-b12; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.7.0
[2020-07-22 17:20:55,659] safe_subprocess.py [ERROR] > INFO 2020-07-22 17:20:55 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT.
[2020-07-22 17:20:55,659] safe_subprocess.py [ERROR] > INFO 2020-07-22 17:20:55 CrosscheckFingerprints Fingerprinting 1 INPUT files.
[2020-07-22 17:20:55,660] safe_subprocess.py [ERROR] > INFO 2020-07-22 17:20:55 FingerprintChecker Processed files. 1 fingerprints found in map.
[2020-07-22 17:20:55,660] safe_subprocess.py [ERROR] > INFO 2020-07-22 17:20:55 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files.
[2020-07-22 17:20:55,661] safe_subprocess.py [ERROR] > INFO 2020-07-22 17:20:55 FingerprintChecker Processed files. 1 fingerprints found in map.
[2020-07-22 17:20:55,661] safe_subprocess.py [ERROR] > INFO 2020-07-22 17:20:55 CrosscheckFingerprints Checking each READGROUP in INPUT with each READGROUP in SECOND_INPUT.
[2020-07-22 17:20:55,662] safe_subprocess.py [ERROR] > ERROR 2020-07-22 17:20:55 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites
[2020-07-22 17:20:55,662] safe_subprocess.py [ERROR] > [Wed Jul 22 17:20:55 UTC 2020] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes.
[2020-07-22 17:20:55,662] safe_subprocess.py [ERROR] > Runtime.totalMemory()=262668288
[2020-07-22 17:20:55,663] safe_subprocess.py [ERROR] > To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

[2020-07-22 17:20:55,663] gatk.py [ERROR] > Exit code 4 caught from tool GATK