Hello everyone,

I am using GATK v4.2.3.0. I have already checked the previous post for the same error. I have tried everything that the user has tried, but I still get the error.

Command-

/home/vishak/GATK/gatk-4.2.3.0/gatk BaseRecalibrator -I NA12878_duplicate_merged.bam -R /home/vishak/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa -O recalibration.table --known-sites /home/vishak/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf --known-sites /home/vishak/SNV-file/Homo_sapiens_assembly38.known_indels.vcf --known-sites /home/vishak/SNV-file/Mills_and_1000G_gold_standard.indels.hg38.vcf --known-sites /home/vishak/SNV-file/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf --known-sites /home/vishak/SNV-file/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf.gz

Full Log-

Using GATK jar /home/vishak/GATK/gatk-4.2.3.0/gatk-package-4.2.3.0-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 /home/vishak/GATK/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar BaseRecalibrator -I NA12878_duplicate_merged.bam -R /home/vishak/ref-gen/GRCh38_full_analysis_set_plus_decoy_hla.fa -O recalibration.table --known-sites /home/vishak/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf --known-sites /home/vishak/SNV-file/Homo_sapiens_assembly38.known_indels.vcf --known-sites /home/vishak/SNV-file/Mills_and_1000G_gold_standard.indels.hg38.vcf --known-sites /home/vishak/SNV-file/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf --known-sites /home/vishak/SNV-file/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf.gz
10:31:19.529 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/vishak/GATK/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 20, 2021 10:31:19 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:31:19.848 INFO BaseRecalibrator - ------------------------------------------------------------
10:31:19.848 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.3.0
10:31:19.848 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
10:31:19.848 INFO BaseRecalibrator - Executing as vishak@cbr1 on Linux v5.11.0-41-generic amd64
10:31:19.848 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v11.0.13+8-Ubuntu-0ubuntu1.20.04
10:31:19.849 INFO BaseRecalibrator - Start Date/Time: 20 December 2021 at 10:31:19 AM IST
10:31:19.849 INFO BaseRecalibrator - ------------------------------------------------------------
10:31:19.849 INFO BaseRecalibrator - ------------------------------------------------------------
10:31:19.849 INFO BaseRecalibrator - HTSJDK Version: 2.24.1
10:31:19.850 INFO BaseRecalibrator - Picard Version: 2.25.4
10:31:19.850 INFO BaseRecalibrator - Built for Spark Version: 2.4.5
10:31:19.850 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:31:19.850 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:31:19.850 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:31:19.850 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:31:19.850 INFO BaseRecalibrator - Deflater: IntelDeflater
10:31:19.850 INFO BaseRecalibrator - Inflater: IntelInflater
10:31:19.850 INFO BaseRecalibrator - GCS max retries/reopens: 20
10:31:19.850 INFO BaseRecalibrator - Requester pays: disabled
10:31:19.851 INFO BaseRecalibrator - Initializing engine
10:31:20.214 INFO FeatureManager - Using codec VCFCodec to read file file:///home/vishak/SNV-file/Homo_sapiens_assembly38.dbsnp138.vcf
10:31:20.373 INFO FeatureManager - Using codec VCFCodec to read file file:///home/vishak/SNV-file/Homo_sapiens_assembly38.known_indels.vcf
10:31:20.423 INFO FeatureManager - Using codec VCFCodec to read file file:///home/vishak/SNV-file/Mills_and_1000G_gold_standard.indels.hg38.vcf
10:31:20.510 INFO FeatureManager - Using codec VCFCodec to read file file:///home/vishak/SNV-file/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf
10:31:20.600 INFO FeatureManager - Using codec VCFCodec to read file file:///home/vishak/SNV-file/resources_broad_hg38_v0_1000G_omni2.5.hg38.vcf.gz
10:31:20.858 INFO BaseRecalibrator - Done initializing engine
10:31:20.861 INFO BaseRecalibrationEngine - The covariates being used here:
10:31:20.861 INFO BaseRecalibrationEngine - ReadGroupCovariate
10:31:20.861 INFO BaseRecalibrationEngine - QualityScoreCovariate
10:31:20.861 INFO BaseRecalibrationEngine - ContextCovariate
10:31:20.861 INFO BaseRecalibrationEngine - CycleCovariate
10:31:20.951 INFO ProgressMeter - Starting traversal
10:31:20.951 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
10:31:20.977 INFO BaseRecalibrator - Shutting down engine
[20 December 2021 at 10:31:20 AM IST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1270874112
java.lang.NullPointerException
at org.broadinstitute.hellbender.utils.recalibration.RecalUtils.parsePlatformForRead(RecalUtils.java:495)
at org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.processRead(BaseRecalibrationEngine.java:124)
at org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator.apply(BaseRecalibrator.java:189)
at org.broadinstitute.hellbender.engine.ReadWalker.lambda$traverse$0(ReadWalker.java:100)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
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:497)
at org.broadinstitute.hellbender.engine.ReadWalker.traverse(ReadWalker.java:98)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

Similar to the previous post, I tried re-indexing the reference genome. I used ValidateSamFiles which did not show any warning or errors. The input file is also coordinate sorted. There does not seem to be any issues with Read Groups also.

I do not think the problem arises from the vcf files I have given as known-sites since my other sample works with it. If it helps, I am using the SRR622457 files. I appreciate any kind of help!