gatk
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20 hours ago •
broadinstitute
broadinstitute
GATK4.5.0.0 HaplotypeCaller exits with error code 245 while no error message
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
