GATK version used: gatk-4.4.0.0

Exact command used: 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 /gpfs/data/apps/soft/gatk-4.4.0.0/gatk/build/libs/gatk-package-4.4.0.0-51-ga8b4145-SNAPSHOT-local.jar VariantAnnotator -R /gpfs/genetics/ngs/test_run/GRCh38_full_analysis_set_plus_decoy_hla.fa -V /gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_genotypegvcfs/TLSA_genotypegvcfs_chr21.vcf -O /gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_VA/TLSA_Variantannotator_chr21.vcf -A AlleleFraction -A BaseQuality -A ChromosomeCounts -A ClippingRankSumTest -A CountNs -A Coverage -A DepthPerAlleleBySample -A DepthPerSampleHC -A FragmentLength -A GenotypeSummaries -A LikelihoodRankSumTest -A MappingQuality -A MappingQualityRankSumTest -A MappingQualityZero -A OrientationBiasReadCounts -A OriginalAlignment -A PossibleDeNovo -A QualByDepth -A ReadPosition -A ReadPosRankSumTest -A RMSMappingQuality -A TandemRepeat -A UniqueAltReadCount --dbsnp /gpfs/data/user/siddhi/ngs/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf

Entire program log:
14:34:47.619 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/data/apps/soft/gatk-4.4.0.0/gatk/build/libs/gatk-package-4.4.0.0-51-ga8b4145-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:34:47.648 INFO  VariantAnnotator - ------------------------------------------------------------
14:34:47.650 INFO  VariantAnnotator - The Genome Analysis Toolkit (GATK) v4.4.0.0-51-ga8b4145-SNAPSHOT
14:34:47.650 INFO  VariantAnnotator - For support and documentation go to https://software.broadinstitute.org/gatk/
14:34:47.650 INFO  VariantAnnotator - Executing as siddhi@node46 on Linux v3.10.0-957.el7.x86_64 amd64
14:34:47.650 INFO  VariantAnnotator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.2+8-LTS-86
14:34:47.650 INFO  VariantAnnotator - Start Date/Time: December 4, 2024 at 2:34:47 PM IST
14:34:47.650 INFO  VariantAnnotator - ------------------------------------------------------------
14:34:47.650 INFO  VariantAnnotator - ------------------------------------------------------------
14:34:47.651 INFO  VariantAnnotator - HTSJDK Version: 3.0.5
14:34:47.651 INFO  VariantAnnotator - Picard Version: 3.0.0
14:34:47.651 INFO  VariantAnnotator - Built for Spark Version: 3.3.1
14:34:47.651 INFO  VariantAnnotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:34:47.651 INFO  VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:34:47.651 INFO  VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:34:47.652 INFO  VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:34:47.652 INFO  VariantAnnotator - Deflater: IntelDeflater
14:34:47.652 INFO  VariantAnnotator - Inflater: IntelInflater
14:34:47.652 INFO  VariantAnnotator - GCS max retries/reopens: 20
14:34:47.652 INFO  VariantAnnotator - Requester pays: disabled
14:34:47.652 INFO  VariantAnnotator - Initializing engine
14:34:47.935 INFO  FeatureManager - Using codec VCFCodec to read file file:///gpfs/data/user/siddhi/ngs/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf
14:34:48.134 INFO  FeatureManager - Using codec VCFCodec to read file file:///gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_genotypegvcfs/TLSA_genotypegvcfs_chr21.vcf
14:34:48.233 INFO  VariantAnnotator - Done initializing engine
14:34:48.354 INFO  ProgressMeter - Starting traversal
14:34:48.355 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
14:34:48.474 WARN  VariantAnnotatorEngine - Jumbo genotype annotations requested but fragment likelihoods or haplotype likelihoods were not given.
14:34:48.484 WARN  DepthPerSampleHC - Annotation will not be calculated at position chr21:5030088 and possibly subsequent; genotype for sample 001MS is not called
14:34:48.737 WARN  OriginalAlignment - One or more variant contexts is missing the 'TLOD' annotation, OCM will not be computed for these VariantContexts
14:38:24.631 INFO  ProgressMeter -        chr21:5119314              3.6                  1000            277.4
14:42:09.260 INFO  ProgressMeter -        chr21:5223262              7.3                  2000            272.2
14:46:19.055 INFO  ProgressMeter -        chr21:5231426             11.5                  3000            260.6
14:50:15.937 INFO  ProgressMeter -        chr21:5242628             15.5                  4000            258.7
14:54:08.883 INFO  ProgressMeter -        chr21:5254674             19.3                  5000            258.5
14:57:18.130 INFO  ProgressMeter -        chr21:5276312             22.5                  6000            266.7
15:00:43.104 INFO  ProgressMeter -        chr21:5293511             25.9                  7000            270.1
15:04:33.648 INFO  ProgressMeter -        chr21:5304912             29.8                  8000            268.9
15:08:25.588 INFO  ProgressMeter -        chr21:5314199             33.6                  9000            267.7
15:12:24.561 INFO  ProgressMeter -        chr21:5321580             37.6                 10000            265.9
15:16:16.787 INFO  ProgressMeter -        chr21:5329658             41.5                 11000            265.2
15:19:51.918 INFO  ProgressMeter -        chr21:5349291             45.1                 12000            266.3
15:23:22.238 INFO  ProgressMeter -        chr21:5367960             48.6                 13000            267.7
15:27:02.306 INFO  ProgressMeter -        chr21:5382664             52.2                 14000            268.0
15:30:25.084 INFO  ProgressMeter -        chr21:6078494             55.6                 15000            269.7
15:33:50.759 INFO  ProgressMeter -        chr21:6369171             59.0                 16000            271.0
15:37:12.498 INFO  ProgressMeter -        chr21:6489290             62.4                 17000            272.4
15:40:18.153 INFO  ProgressMeter -        chr21:6851957             65.5                 18000            274.8
15:43:35.037 INFO  ProgressMeter -        chr21:7211952             68.8                 19000            276.3
15:47:24.491 INFO  ProgressMeter -        chr21:7235509             72.6                 20000            275.5
15:51:20.640 INFO  ProgressMeter -        chr21:7245715             76.5                 21000            274.4
15:55:16.852 INFO  ProgressMeter -        chr21:7254317             80.5                 22000            273.4
15:59:19.869 INFO  ProgressMeter -        chr21:7259928             84.5                 23000            272.1
16:03:19.950 INFO  ProgressMeter -        chr21:7274104             88.5                 24000            271.1
16:07:14.691 INFO  ProgressMeter -        chr21:7290121             92.4                 25000            270.4
16:11:07.494 INFO  ProgressMeter -        chr21:7306486             96.3                 26000            269.9
16:15:02.878 INFO  ProgressMeter -        chr21:7321842            100.2                 27000            269.3
16:18:46.323 INFO  ProgressMeter -        chr21:7916514            104.0                 28000            269.3
16:22:54.776 INFO  ProgressMeter -        chr21:7923290            108.1                 29000            268.3
16:27:08.214 INFO  ProgressMeter -        chr21:7929555            112.3                 30000            267.1
16:31:14.779 INFO  ProgressMeter -        chr21:7935241            116.4                 31000            266.2
16:35:23.784 INFO  ProgressMeter -        chr21:7940363            120.6                 32000            265.4
16:39:35.208 INFO  ProgressMeter -        chr21:7945890            124.8                 33000            264.5
16:43:56.147 INFO  ProgressMeter -        chr21:7951065            129.1                 34000            263.3
16:48:06.444 INFO  ProgressMeter -        chr21:7956272            133.3                 35000            262.6
16:52:12.030 INFO  ProgressMeter -        chr21:7962616            137.4                 36000            262.0
16:56:11.195 INFO  ProgressMeter -        chr21:7969521            141.4                 37000            261.7
17:00:07.390 INFO  ProgressMeter -        chr21:7975934            145.3                 38000            261.5
17:03:51.265 INFO  ProgressMeter -        chr21:7993360            149.0                 39000            261.7
17:07:31.774 INFO  ProgressMeter -        chr21:8005554            152.7                 40000            261.9
17:11:07.743 INFO  ProgressMeter -        chr21:8013766            156.3                 41000            262.3
17:14:46.303 INFO  ProgressMeter -        chr21:8020892            160.0                 42000            262.6
17:18:23.499 INFO  ProgressMeter -        chr21:8031714            163.6                 43000            262.9
17:22:16.985 INFO  ProgressMeter -        chr21:8037883            167.5                 44000            262.7
17:26:05.419 INFO  ProgressMeter -        chr21:8045192            171.3                 45000            262.7
17:30:06.028 INFO  ProgressMeter -        chr21:8217265            175.3                 46000            262.4
17:34:28.821 INFO  ProgressMeter -        chr21:8233063            179.7                 47000            261.6
17:38:11.327 INFO  ProgressMeter -        chr21:8411557            183.4                 48000            261.7
17:42:06.084 INFO  ProgressMeter -        chr21:8527383            187.3                 49000            261.6
17:45:44.619 INFO  ProgressMeter -        chr21:8554865            190.9                 50000            261.9
17:49:15.084 INFO  ProgressMeter -        chr21:8591494            194.4                 51000            262.3
17:52:20.732 INFO  ProgressMeter -        chr21:8622393            197.5                 52000            263.2
17:55:27.442 INFO  ProgressMeter -        chr21:8671773            200.7                 53000            264.1
17:59:12.318 INFO  ProgressMeter -        chr21:8695231            204.4                 54000            264.2
18:03:07.877 INFO  ProgressMeter -        chr21:8760948            208.3                 55000            264.0
18:07:06.765 INFO  ProgressMeter -        chr21:8770328            212.3                 56000            263.8
18:11:02.522 INFO  ProgressMeter -        chr21:8781623            216.2                 57000            263.6
18:15:02.190 INFO  ProgressMeter -        chr21:8791964            220.2                 58000            263.4
18:18:49.532 INFO  ProgressMeter -        chr21:8809247            224.0                 59000            263.4
18:22:48.458 INFO  ProgressMeter -        chr21:8819375            228.0                 60000            263.2
18:26:37.444 INFO  ProgressMeter -        chr21:8835831            231.8                 61000            263.1
18:30:30.555 INFO  ProgressMeter -        chr21:8851110            235.7                 62000            263.0
18:34:04.861 INFO  ProgressMeter -        chr21:8987176            239.3                 63000            263.3
18:38:10.610 INFO  ProgressMeter -        chr21:8991993            243.4                 64000            263.0
18:42:14.585 INFO  ProgressMeter -        chr21:8997927            247.4                 65000            262.7
18:46:14.832 INFO  ProgressMeter -        chr21:9004213            251.4                 66000            262.5
18:50:13.355 INFO  ProgressMeter -        chr21:9011642            255.4                 67000            262.3
18:54:09.552 INFO  ProgressMeter -        chr21:9020152            259.4                 68000            262.2
18:58:13.512 INFO  ProgressMeter -        chr21:9028961            263.4                 69000            261.9
19:02:13.244 INFO  ProgressMeter -        chr21:9038723            267.4                 70000            261.8
19:06:05.565 INFO  ProgressMeter -        chr21:9055083            271.3                 71000            261.7
19:09:52.792 INFO  ProgressMeter -        chr21:9076076            275.1                 72000            261.7
19:13:35.295 INFO  ProgressMeter -        chr21:9094198            278.8                 73000            261.9
19:17:17.913 INFO  ProgressMeter -        chr21:9107962            282.5                 74000            262.0
19:20:56.790 INFO  ProgressMeter -        chr21:9124001            286.1                 75000            262.1
19:24:42.950 INFO  ProgressMeter -        chr21:9137154            289.9                 76000            262.2
19:28:10.730 INFO  ProgressMeter -        chr21:9151601            293.4                 77000            262.5
19:31:47.072 INFO  ProgressMeter -        chr21:9166897            297.0                 78000            262.6
19:35:29.905 INFO  ProgressMeter -        chr21:9183275            300.7                 79000            262.7
19:39:15.048 INFO  ProgressMeter -        chr21:9246250            304.4                 80000            262.8
19:43:06.814 INFO  ProgressMeter -        chr21:9269355            308.3                 81000            262.7
19:46:52.938 INFO  ProgressMeter -        chr21:9296715            312.1                 82000            262.8
19:50:49.392 INFO  ProgressMeter -        chr21:9312142            316.0                 83000            262.6
19:54:35.382 INFO  ProgressMeter -        chr21:9330617            319.8                 84000            262.7
19:58:25.075 INFO  ProgressMeter -        chr21:9349702            323.6                 85000            262.7
20:02:18.443 INFO  ProgressMeter -        chr21:9364344            327.5                 86000            262.6
20:06:06.352 INFO  ProgressMeter -        chr21:9537520            331.3                 87000            262.6
20:10:00.586 INFO  ProgressMeter -        chr21:9562872            335.2                 88000            262.5
20:13:57.220 INFO  ProgressMeter -        chr21:9574811            339.1                 89000            262.4
20:17:51.123 INFO  ProgressMeter -        chr21:9586115            343.0                 90000            262.4
20:21:45.089 INFO  ProgressMeter -        chr21:9599644            346.9                 91000            262.3
20:25:39.912 INFO  ProgressMeter -        chr21:9621214            350.9                 92000            262.2
20:29:33.741 INFO  ProgressMeter -        chr21:9644884            354.8                 93000            262.2
20:33:27.441 INFO  ProgressMeter -        chr21:9662995            358.7                 94000            262.1
20:37:18.801 INFO  ProgressMeter -        chr21:9685764            362.5                 95000            262.1
20:41:10.578 INFO  ProgressMeter -        chr21:9710427            366.4                 96000            262.0
20:45:06.680 INFO  ProgressMeter -        chr21:9728891            370.3                 97000            261.9
20:49:01.743 INFO  ProgressMeter -        chr21:9743239            374.2                 98000            261.9
20:52:57.073 INFO  ProgressMeter -        chr21:9757331            378.1                 99000            261.8
20:57:01.280 INFO  ProgressMeter -        chr21:9771411            382.2                100000            261.6
21:00:58.522 INFO  ProgressMeter -        chr21:9786718            386.2                101000            261.5
21:04:52.776 INFO  ProgressMeter -        chr21:9805731            390.1                102000            261.5
21:08:46.492 INFO  ProgressMeter -        chr21:9813980            394.0                103000            261.4
21:12:44.396 INFO  ProgressMeter -        chr21:9817457            397.9                104000            261.3
21:16:37.255 INFO  ProgressMeter -        chr21:9821049            401.8                105000            261.3
21:20:40.159 INFO  ProgressMeter -        chr21:9824199            405.9                106000            261.2
21:24:11.233 INFO  ProgressMeter -        chr21:9833027            409.4                107000            261.4
21:27:55.991 INFO  ProgressMeter -        chr21:9839379            413.1                108000            261.4
21:31:50.906 INFO  ProgressMeter -        chr21:9852150            417.0                109000            261.4
21:35:43.646 INFO  ProgressMeter -        chr21:9864541            420.9                110000            261.3
21:39:41.850 INFO  ProgressMeter -        chr21:9877952            424.9                111000            261.2
21:43:39.076 INFO  ProgressMeter -        chr21:9890437            428.8                112000            261.2
21:47:35.309 INFO  ProgressMeter -        chr21:9905487            432.8                113000            261.1
21:51:30.990 INFO  ProgressMeter -        chr21:9920193            436.7                114000            261.0
21:55:26.873 INFO  ProgressMeter -        chr21:9935618            440.6                115000            261.0
21:59:22.356 INFO  ProgressMeter -        chr21:9950193            444.6                116000            260.9
22:03:17.004 INFO  ProgressMeter -        chr21:9966451            448.5                117000            260.9
22:07:15.954 INFO  ProgressMeter -        chr21:9982711            452.5                118000            260.8
22:11:11.113 INFO  ProgressMeter -       chr21:10000362            456.4                119000            260.7
22:15:06.762 INFO  ProgressMeter -       chr21:10018672            460.3                120000            260.7
22:19:01.072 INFO  ProgressMeter -       chr21:10043443            464.2                121000            260.7
22:22:53.280 INFO  ProgressMeter -       chr21:10074813            468.1                122000            260.6
22:26:48.664 INFO  ProgressMeter -       chr21:10102996            472.0                123000            260.6
22:30:48.433 INFO  ProgressMeter -       chr21:10127658            476.0                124000            260.5
22:34:41.988 INFO  ProgressMeter -       chr21:10152628            479.9                125000            260.5
22:38:33.198 INFO  ProgressMeter -       chr21:10271625            483.7                126000            260.5
22:41:42.189 INFO  VariantAnnotator - Shutting down engine
[December 4, 2024 at 10:41:42 PM IST] org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator done. Elapsed time: 486.91 minutes.
Runtime.totalMemory()=1291845632
java.lang.IllegalArgumentException: Ref and alt alleles have same last base, hence this event is not in its minimal representation.
    at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:798)
    at org.broadinstitute.hellbender.utils.haplotype.Event.<init>(Event.java:31)
    at org.broadinstitute.hellbender.utils.haplotype.Event.ofWithoutAttributes(Event.java:42)
    at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
    at java.base/java.util.Collections$2.tryAdvance(Collections.java:4853)
    at java.base/java.util.Collections$2.forEachRemaining(Collections.java:4861)
    at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
    at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
    at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
    at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
    at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.splitVariantContextToEvents(GATKVariantContextUtils.java:1723)
    at org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator.getRsID(VariantOverlapAnnotator.java:178)
    at org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator.annotateRsID(VariantOverlapAnnotator.java:77)
    at org.broadinstitute.hellbender.tools.walkers.annotator.VariantOverlapAnnotator.annotateRsID(VariantOverlapAnnotator.java:63)
    at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:370)
    at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:334)
    at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator.apply(VariantAnnotator.java:243)
    at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
    at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
    at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
    at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
    at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
    at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
    at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
    at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
    at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
    at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
    at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
    at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
    at org.broadinstitute.hellbender.Main.main(Main.java:306)
Using GATK jar /gpfs/data/apps/soft/gatk-4.4.0.0/gatk/build/libs/gatk-package-4.4.0.0-51-ga8b4145-SNAPSHOT-local.jar defined in environment variable GATK_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 /gpfs/data/apps/soft/gatk-4.4.0.0/gatk/build/libs/gatk-package-4.4.0.0-51-ga8b4145-SNAPSHOT-local.jar VariantAnnotator -R /gpfs/genetics/ngs/test_run/GRCh38_full_analysis_set_plus_decoy_hla.fa -V /gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_genotypegvcfs/TLSA_genotypegvcfs_chr21.vcf -O /gpfs/gidata/genomeindia/siddhi/Jointcall/TLSA_VA/TLSA_Variantannotator_chr21.vcf -A AlleleFraction -A BaseQuality -A ChromosomeCounts -A ClippingRankSumTest -A CountNs -A Coverage -A DepthPerAlleleBySample -A DepthPerSampleHC -A FragmentLength -A GenotypeSummaries -A LikelihoodRankSumTest -A MappingQuality -A MappingQualityRankSumTest -A MappingQualityZero -A OrientationBiasReadCounts -A OriginalAlignment -A PossibleDeNovo -A QualByDepth -A ReadPosition -A ReadPosRankSumTest -A RMSMappingQuality -A TandemRepeat -A UniqueAltReadCount --dbsnp /gpfs/data/user/siddhi/ngs/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf