GATK4.5.0.0 HaplotypeCaller exits with error code 245 while no error message

[Alipha-Clisa]

Greetings,
I am trying to use hifi long reads identifying the SNVs, but I have noticed that the GATK would work normally on some part of chromosome, while terminates while processing other chromosome area, with no error message.
A dev-member has recommended to scoop out the specific area would leading to failure, but I wonder whether there is a way to fix it? since the break points is too many to be excluded. Nearly within a 20M region is there a breakpoint needed to be scooped out just on a single chromosome, nor do I want to interrupt the continuity of SNVs.
Best

Using GATK jar /data/tcq/softwares_bio/bin/gatk-package-4.5.0.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /data/tcq/softwares_bio/bin/gatk-package-4.5.0.0-local.jar HaplotypeCaller -R ./reference_chr1A.fasta -I ./sample_chr1A_markdup.bam -O ./sample_chr1A_part11.vcf.gz -L chr1A:100000000-110000000 --create-output-variant-index false
20:13:22.002 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/tcq/softwares_bio/bin/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
20:13:22.533 INFO  HaplotypeCaller - ------------------------------------------------------------
20:13:22.541 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.5.0.0
20:13:22.541 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
20:13:22.541 INFO  HaplotypeCaller - Executing as [email protected] on Linux v4.18.0-544.el8.x86_64 amd64
20:13:22.541 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v21.0.2+13-58
20:13:22.542 INFO  HaplotypeCaller - Start Date/Time: February 27, 2025, 8:13:21 PM CST
20:13:22.542 INFO  HaplotypeCaller - ------------------------------------------------------------
20:13:22.542 INFO  HaplotypeCaller - ------------------------------------------------------------
20:13:22.550 INFO  HaplotypeCaller - HTSJDK Version: 4.1.0
20:13:22.550 INFO  HaplotypeCaller - Picard Version: 3.1.1
20:13:22.550 INFO  HaplotypeCaller - Built for Spark Version: 3.5.0
20:13:22.551 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:13:22.551 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:13:22.551 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:13:22.551 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:13:22.552 INFO  HaplotypeCaller - Deflater: IntelDeflater
20:13:22.552 INFO  HaplotypeCaller - Inflater: IntelInflater
20:13:22.552 INFO  HaplotypeCaller - GCS max retries/reopens: 20
20:13:22.552 INFO  HaplotypeCaller - Requester pays: disabled
20:13:22.553 INFO  HaplotypeCaller - Initializing engine
20:13:22.842 INFO  IntervalArgumentCollection - Processing 10000001 bp from intervals
20:13:22.850 INFO  HaplotypeCaller - Done initializing engine
20:13:22.868 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/data/tcq/softwares_bio/bin/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
20:13:22.870 INFO  NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/data/tcq/softwares_bio/bin/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
20:13:22.874 INFO  IntelSmithWaterman - Using CPU-supported AVX-512 instructions
20:13:22.874 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:13:22.878 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:13:22.894 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/data/tcq/softwares_bio/bin/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
20:13:22.926 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions
20:13:22.927 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:13:22.927 INFO  IntelPairHmm - Available threads: 80
20:13:22.927 INFO  IntelPairHmm - Requested threads: 4
20:13:22.928 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:13:23.038 INFO  ProgressMeter - Starting traversal
20:13:23.039 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
20:13:24.714 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1A:100002327 and possibly subsequent; at least 10 samples must have called genotypes
20:13:36.243 INFO  ProgressMeter -      chr1A:100030675              0.2                   140            636.2
20:13:47.983 INFO  ProgressMeter -      chr1A:100038089              0.4                   180            433.0
20:13:58.063 INFO  ProgressMeter -      chr1A:100121053              0.6                   540            925.1
20:14:09.843 INFO  ProgressMeter -      chr1A:100165706              0.8                   740            948.6
20:14:22.538 INFO  ProgressMeter -      chr1A:100167372              1.0                   750            756.3
20:14:41.349 INFO  ProgressMeter -      chr1A:100170913              1.3                   770            590.0
20:14:52.156 INFO  ProgressMeter -      chr1A:100172820              1.5                   780            525.3
20:15:03.348 INFO  ProgressMeter -      chr1A:100174577              1.7                   790            472.5
20:15:13.364 INFO  ProgressMeter -      chr1A:100179044              1.8                   810            440.5
20:15:23.399 INFO  ProgressMeter -      chr1A:100280978              2.0                  1250            623.1
20:15:37.073 INFO  ProgressMeter -      chr1A:100350498              2.2                  1560            698.3
20:15:48.360 INFO  ProgressMeter -      chr1A:100371036              2.4                  1670            689.5
20:16:02.030 INFO  ProgressMeter -      chr1A:100438583              2.6                  1970            743.4
20:16:12.341 INFO  ProgressMeter -      chr1A:100467942              2.8                  2130            754.9
20:16:24.701 INFO  ProgressMeter -      chr1A:100488004              3.0                  2220            733.2
20:16:36.521 INFO  ProgressMeter -      chr1A:100492812              3.2                  2250            697.7
20:16:46.992 INFO  ProgressMeter -      chr1A:100515619              3.4                  2350            691.3
20:16:57.106 INFO  ProgressMeter -      chr1A:100618610              3.6                  2800            784.8
20:17:08.554 INFO  ProgressMeter -      chr1A:100624020              3.8                  2830            752.9
20:17:21.619 INFO  ProgressMeter -      chr1A:100630964              4.0                  2870            721.8
20:17:32.207 INFO  ProgressMeter -      chr1A:100689969              4.2                  3150            758.5
20:17:43.280 INFO  ProgressMeter -      chr1A:100700093              4.3                  3220            742.4
20:17:54.312 INFO  ProgressMeter -      chr1A:100714619              4.5                  3320            734.3
20:18:04.354 INFO  ProgressMeter -      chr1A:100784073              4.7                  3660            780.6
20:18:14.867 INFO  ProgressMeter -      chr1A:100857039              4.9                  4010            824.5
20:18:25.751 INFO  ProgressMeter -      chr1A:100863943              5.0                  4050            802.7
20:18:35.813 INFO  ProgressMeter -      chr1A:100903626              5.2                  4240            813.4
20:18:46.296 INFO  ProgressMeter -      chr1A:100947141              5.4                  4450            826.0
20:18:56.452 INFO  ProgressMeter -      chr1A:101043333              5.6                  4870            876.4
20:19:06.461 INFO  ProgressMeter -      chr1A:101098928              5.7                  5120            894.5
20:19:19.854 INFO  ProgressMeter -      chr1A:101114921              5.9                  5210            876.1
20:19:31.766 INFO  ProgressMeter -      chr1A:101119854              6.1                  5240            852.7
20:19:45.915 INFO  ProgressMeter -      chr1A:101132792              6.4                  5300            830.6
20:19:56.090 INFO  ProgressMeter -      chr1A:101159159              6.6                  5410            825.8
20:20:07.705 INFO  ProgressMeter -      chr1A:101216228              6.7                  5660            839.2
20:20:18.577 INFO  ProgressMeter -      chr1A:101221562              6.9                  5700            823.0
20:20:30.437 INFO  ProgressMeter -      chr1A:101228312              7.1                  5740            805.8
20:20:41.147 INFO  ProgressMeter -      chr1A:101290304              7.3                  6090            834.0
20:20:51.148 INFO  ProgressMeter -      chr1A:101363549              7.5                  6420            859.6
20:21:02.833 INFO  ProgressMeter -      chr1A:101377988              7.7                  6490            846.9
20:21:12.843 INFO  ProgressMeter -      chr1A:101450578              7.8                  6810            869.7
20:21:22.888 INFO  ProgressMeter -      chr1A:101506111              8.0                  7050            881.5
20:21:37.759 INFO  ProgressMeter -      chr1A:101510971              8.2                  7080            858.7
20:21:48.272 INFO  ProgressMeter -      chr1A:101521084              8.4                  7160            850.3
20:22:00.801 INFO  ProgressMeter -      chr1A:101528634              8.6                  7220            836.7
20:22:10.970 INFO  ProgressMeter -      chr1A:101534885              8.8                  7270            826.2
20:22:22.358 INFO  ProgressMeter -      chr1A:101539889              9.0                  7310            813.2
20:22:33.590 INFO  ProgressMeter -      chr1A:101570952              9.2                  7460            813.0
20:22:43.716 INFO  ProgressMeter -      chr1A:101628518              9.3                  7720            826.1
20:22:54.973 INFO  ProgressMeter -      chr1A:101691579              9.5                  8040            843.5
20:23:05.876 INFO  ProgressMeter -      chr1A:101772458              9.7                  8400            864.7
20:23:16.498 INFO  ProgressMeter -      chr1A:101776251              9.9                  8430            852.3
20:23:27.649 INFO  ProgressMeter -      chr1A:101791407             10.1                  8510            844.5
20:23:39.469 INFO  ProgressMeter -      chr1A:101853064             10.3                  8770            853.6
20:23:50.708 INFO  ProgressMeter -      chr1A:101858558             10.5                  8810            842.2
20:24:01.648 INFO  ProgressMeter -      chr1A:101892464             10.6                  8980            843.7
20:24:11.889 INFO  ProgressMeter -      chr1A:101966039             10.8                  9290            859.1
20:24:27.764 INFO  ProgressMeter -      chr1A:101999534             11.1                  9430            851.2
20:24:38.284 INFO  ProgressMeter -      chr1A:102003459             11.3                  9450            839.7
20:24:54.277 INFO  ProgressMeter -      chr1A:102033113             11.5                  9590            832.4
20:25:09.730 INFO  ProgressMeter -      chr1A:102037312             11.8                  9610            815.9
20:25:21.193 INFO  ProgressMeter -      chr1A:102064600             12.0                  9750            814.6