I am trying to run CrosscheckFingerprints on multiple BAM files from the same individual to confirm all BAM files are likely from the same subject. I'm following the example in the section with this description: Check that all the readgroups match as expected when providing reads from two samples from the same individual.

When I run the command with two samples I know are from different individuals, the output correctly identifies them as a MISMATCH. However, when I run the command with samples from the same individual, the comparison is also identified as a MISMATCH, but the LOD scores are closer to 0. The LOD scores I get for known mismatches are roughly between -1400 and -1600. The LOD scores I get for comparisons between different samples from the same individual are between -500 and -100. 

I am using bulk RNAseq data and the pre-computed haplotype map from https://github.com/naumanjaved/fingerprint_maps.

Can someone help troubleshoot why expected MATCHES are performing better than known MISMATCHES but are still not being identified as MATCHES or even INCONCLUSIVE? 

Required information is below. 

Thank you in advance,

Chris

REQUIRED for all errors and issues:
a) GATK version used: Picard version 2.26.11-SNAPSHOT

b) Exact command used:

java -jar build/libs/picard.jar CrosscheckFingerprints \
    -INPUT ../bam/F4196374_1001.bam \
    -INPUT ../bam/F4196593_1001.bam \
    -HAPLOTYPE_MAP hg38_nochr.map \
    -LOD_THRESHOLD -5 \
    -CROSSCHECK_BY FILE \
    -EXPECT_ALL_GROUPS_TO_MATCH true \
    -OUTPUT all_files.crosscheck_metrics

c) Entire program log:

### log to stdout ###############

14:35:42.550 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/domino/datasets/local/RSEM_Index/picard/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Mar 23 14:35:42 UTC 2022] CrosscheckFingerprints --INPUT ../bam/F4196374_1001.bam --INPUT ../bam/F4196593_1001.bam --OUTPUT all_files.crosscheck_metrics --HAPLOTYPE_MAP hg38_nochr.map --LOD_THRESHOLD -5.0 --CROSSCHECK_BY FILE --EXPECT_ALL_GROUPS_TO_MATCH true --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Wed Mar 23 14:35:42 UTC 2022] Executing as ubuntu@run-623b1e4d8755b21bf46d1694-vspqd on Linux 5.4.162-86.275.amzn2.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_242-8u242-b08-0ubuntu3~18.04-b08; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.26.11-SNAPSHOT
INFO    2022-03-23 14:35:42     CrosscheckFingerprints  Fingerprinting 2 INPUT files.
INFO    2022-03-23 14:35:42     FingerprintChecker      Reading an indexed file (file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196374_1001.bam)
INFO    2022-03-23 14:38:15     FingerprintChecker      Reading an indexed file (file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196593_1001.bam)
INFO    2022-03-23 14:40:58     FingerprintChecker      Processed files. 2 fingerprints found in map.
INFO    2022-03-23 14:40:59     CrosscheckFingerprints  Cross-checking all FILE against each other
WARNING 2022-03-23 14:40:59     CrosscheckFingerprints  2 FILEs did not relate as expected.
[Wed Mar 23 14:40:59 UTC 2022] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 5.29 minutes.
Runtime.totalMemory()=11362893824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

##### output file #################

## htsjdk.samtools.metrics.StringHeader
# CrosscheckFingerprints --INPUT ../bam/F4196374_1001.bam --INPUT ../bam/F4196593_1001.bam --OUTPUT all_files.crosscheck_metrics --HAPLOTYPE_MAP hg38_nochr.map --LOD_THRESHOLD -5.0 --CROSSCHECK_BY FILE --EXPECT_ALL_GROUPS_TO_MATCH true --CROSSCHECK_MODE CHECK_SAME_SAMPLE --NUM_THREADS 1 --CALCULATE_TUMOR_AWARE_RESULTS true --ALLOW_DUPLICATE_READS false --GENOTYPING_ERROR_RATE 0.01 --OUTPUT_ERRORS_ONLY false --LOSS_OF_HET_RATE 0.5 --EXIT_CODE_WHEN_MISMATCH 1 --EXIT_CODE_WHEN_NO_VALID_CHECKS 1 --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK 3.0 --TEST_INPUT_READABILITY true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Mar 23 14:35:42 UTC 2022

## METRICS CLASS        picard.fingerprint.CrosscheckMetric
LEFT_GROUP_VALUE        RIGHT_GROUP_VALUE       RESULT  DATA_TYPE       LOD_SCORE       LOD_SCORE_TUMOR_NORMAL  LOD_SCORE_NORMAL_TUMOR  LEFT_RUN_BARCODE        LEFT_LANE       LEFT_MOLECULAR_BARCODE_SEQUENCE LEFT_LIBRARY    LEFT_SAMPLE     LEFT_FILE       RIGHT_RUN_BARCODE       RIGHT_LANE      RIGHT_MOLECULAR_BARCODE_SEQUENCE        RIGHT_LIBRARY   RIGHT_SAMPLE    RIGHT_FILE
file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196374_1001.bam::Sample1       file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196374_1001.bam::Sample1       EXPECTED_MATCH  FILE    2657.792003     2091.069794     2091.069794     ?       -1      ?       1       Sample1 file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196374_1001.bam        ?       -1      ?       1       Sample1 file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196374_1001.bam
file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196374_1001.bam::Sample1       file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196593_1001.bam::Sample2       UNEXPECTED_MISMATCH     FILE    -562.074522     -194.252635     -257.223569     ?       -1      ?       1       Sample1 file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196374_1001.bam        ?       -1      ?       1       Sample2 file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196593_1001.bam
file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196593_1001.bam::Sample2       file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196374_1001.bam::Sample1       UNEXPECTED_MISMATCH     FILE    -562.074522     -257.223569     -194.252635     ?       -1      ?       1       Sample2 file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196593_1001.bam        ?       -1      ?       1       Sample1 file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196374_1001.bam
file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196593_1001.bam::Sample2       file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196593_1001.bam::Sample2       EXPECTED_MATCH  FILE    3187.94952      2504.653897     2504.653897     ?       -1      ?       1       Sample2 file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196593_1001.bam        ?       -1      ?       1       Sample2 file:///domino/datasets/local/RSEM_Index/picard/../bam/F4196593_1001.bam