GenotypeGVCFs error in GATK 4.6.0.0: java.lang.RuntimeException: Invalid deflate block found.

[hxtjc]

I am using the GATK GenotypeGVCFs command to generate vcf through gvcf, but two samples in the same batch of individuals have the following error:

Using GATK jar /share/org/YZWL/yzwl_hanxt/software/gatk-4.6.0.0/gatk-package-4.6.0.0-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 -Xmx60g -jar /share/org/YZWL/yzwl_hanxt/software/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar GenotypeGVCFs -R /share/org/YZWL/yzwl_hanxt/leizhou/ref/ARS1.2_chr30_2.fasta -V H-4.g.vcf.gz -O /share/org/YZWL/yzwl_hanxt/leizhou/variant/temp/H-4.vcf.gz
09:55:48.764 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/org/YZWL/yzwl_hanxt/software/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
09:55:48.863 INFO  GenotypeGVCFs - ------------------------------------------------------------
09:55:48.865 INFO  GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.6.0.0
09:55:48.865 INFO  GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
09:55:48.865 INFO  GenotypeGVCFs - Executing as yzwl_hanxt@c01n0583 on Linux v4.18.0-513.5.1.el8_9.x86_64 amd64
09:55:48.865 INFO  GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.12+8-LTS-286
09:55:48.866 INFO  GenotypeGVCFs - Start Date/Time: September 3, 2024 at 9:55:48 AM CST
09:55:48.866 INFO  GenotypeGVCFs - ------------------------------------------------------------
09:55:48.866 INFO  GenotypeGVCFs - ------------------------------------------------------------
09:55:48.866 INFO  GenotypeGVCFs - HTSJDK Version: 4.1.1
09:55:48.866 INFO  GenotypeGVCFs - Picard Version: 3.2.0
09:55:48.866 INFO  GenotypeGVCFs - Built for Spark Version: 3.5.0
09:55:48.866 INFO  GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:55:48.867 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:55:48.867 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:55:48.867 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:55:48.867 INFO  GenotypeGVCFs - Deflater: IntelDeflater
09:55:48.867 INFO  GenotypeGVCFs - Inflater: IntelInflater
09:55:48.867 INFO  GenotypeGVCFs - GCS max retries/reopens: 20
09:55:48.867 INFO  GenotypeGVCFs - Requester pays: disabled
09:55:48.867 INFO  GenotypeGVCFs - Initializing engine
09:55:49.015 INFO  FeatureManager - Using codec VCFCodec to read file file:///share/org/YZWL/yzwl_hanxt/leizhou/variant/H-4/H-4.g.vcf.gz
09:55:49.190 INFO  GenotypeGVCFs - Done initializing engine
09:55:49.215 INFO  ProgressMeter - Starting traversal
09:55:49.216 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
09:55:49.310 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location chr1_1-157403528:5512 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
09:55:49.336 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1_1-157403528:5512 and possibly subsequent; at least 10 samples must have called genotypes
09:55:50.064 INFO  GenotypeGVCFs - Shutting down engine
[September 3, 2024 at 9:55:50 AM CST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1241513984
java.lang.RuntimeException: Invalid deflate block found.
        at com.intel.gkl.compression.IntelInflater.inflateNative(Native Method)
        at com.intel.gkl.compression.IntelInflater.inflate(IntelInflater.java:176)
        at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:145)
        at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
        at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:561)
        at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:543)
        at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:479)
        at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:469)
        at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:207)
        at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:342)
        at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:268)
        at htsjdk.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:132)
        at htsjdk.tribble.readers.PositionalBufferedStream.read(PositionalBufferedStream.java:84)
        at java.base/sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:270)
        at java.base/sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:313)
        at java.base/sun.nio.cs.StreamDecoder.read(StreamDecoder.java:188)
        at java.base/java.io.InputStreamReader.read(InputStreamReader.java:177)
        at htsjdk.tribble.readers.LongLineBufferedReader.fill(LongLineBufferedReader.java:140)
        at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:300)
        at htsjdk.tribble.readers.LongLineBufferedReader.readLine(LongLineBufferedReader.java:356)
        at htsjdk.tribble.readers.SynchronousLineReader.readLine(SynchronousLineReader.java:51)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:205)
        at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:149)
        at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
        at java.base/java.util.Spliterators$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.forEachOrdered(ReferencePipeline.java:601)
        at org.broadinstitute.hellbender.engine.VariantLocusWalker.traverse(VariantLocusWalker.java:132)
        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)
Job 610777 stderr output:

My command is as follows:

ref=/share/org/YZWL/yzwl_hanxt/leizhou/ref/ARS1.2_chr30_2.fasta
mkdir /share/org/YZWL/yzwl_hanxt/leizhou/variant/temp
cd /share/org/YZWL/yzwl_hanxt/leizhou/variant/H-3
gatk --java-options "-Xmx60g" GenotypeGVCFs \
-R ${ref} \
-V H-3.g.vcf.gz \
-O /share/org/YZWL/yzwl_hanxt/leizhou/variant/temp/H-3.vcf.gz

I have also tried commands like:

ref=/share/org/YZWL/yzwl_hanxt/leizhou/ref/ARS1.2_chr30_2.fasta
mkdir /share/org/YZWL/yzwl_hanxt/leizhou/variant/temp
cd /share/org/YZWL/yzwl_hanxt/leizhou/variant/H-3
gatk --java-options "-Xmx1600g -DGATK_STACKTRACE_ON_USER_EXCEPTION=true"  GenotypeGVCFs \
-R ${ref} \
-V H-3.g.vcf.gz \
-O /share/org/YZWL/yzwl_hanxt/leizhou/variant/temp/H-3.vcf.gz \
--genomicsdb-max-alternate-alleles 10 \
--max-alternate-alleles 4

But it still reports the same error. Could you help me figure out what the problem is? How can I solve it?