Dear GATK team:
I am running the gatk CombineGVCFs program to obtain the GVCF file of a chromosome of 337 samples. However, the task automatically exits after running for a few days. I have not yet found the reason for the error.

REQUIRED for all errors and issues:
a) GATK version used: gatk-4.4.0.0

b) 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 -Xmx240g -Djava.io.tmpdir=/storage/public/home/wgs_wheat/3_bam/tmp -jar /storage/public/apps/software/gatk/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar CombineGVCFs -R /storage/public/home/public_database/wheat_03G_part/iwgsc_refseqv2.1_part_300MB_rename.fa --variant SW001_2B.g.vcf.gz --variant SW002_2B.g.vcf.gz ...(Too many samples, omitted here) --variant SW337_2B.g.vcf.gz -O /storage/public/home/wgs_wheat/4_snp_indel_parallel/Chr2_ALL_GVCF/wgs_chr2_all_sample.g.vcf.gz
c) Entire program log:

... (The previous part is omitted here)
03:56:09.261 INFO  ProgressMeter - Chr2_300000001_600000000:36474997           6685.6           16742435000        2504234.6
03:56:19.282 INFO  ProgressMeter - Chr2_300000001_600000000:36482053           6685.8           16742957000        2504250.1
03:56:29.326 INFO  ProgressMeter - Chr2_300000001_600000000:36491202           6686.0           16743495000        2504267.9
03:56:39.333 INFO  ProgressMeter - Chr2_300000001_600000000:36501617           6686.2           16744105000        2504296.6
03:56:49.338 INFO  ProgressMeter - Chr2_300000001_600000000:36510378           6686.3           16744622000        2504311.5
03:56:58.401 INFO  CombineGVCFs - Shutting down engine
[February 10, 2025, 3:56:58 AM CST] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 6,701.91 minutes.
Runtime.totalMemory()=13321109504
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Communication error on send
    at htsjdk.tribble.readers.SynchronousLineReader.readLine(SynchronousLineReader.java:53)
    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 org.broadinstitute.hellbender.engine.MultiVariantDataSource$1.next(MultiVariantDataSource.java:408)
    at org.broadinstitute.hellbender.engine.MultiVariantDataSource$1.next(MultiVariantDataSource.java:393)
    at htsjdk.samtools.util.PeekableIterator.advance(PeekableIterator.java:71)
    at htsjdk.samtools.util.PeekableIterator.next(PeekableIterator.java:57)
    at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:101)
    at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
    at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1921)
    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.MultiVariantWalker.traverse(MultiVariantWalker.java:136)
    at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:165)
    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:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.io.IOException: Communication error on send
    at java.base/java.io.RandomAccessFile.readBytes0(Native Method)
    at java.base/java.io.RandomAccessFile.readBytes(RandomAccessFile.java:390)
    at java.base/java.io.RandomAccessFile.read(RandomAccessFile.java:424)
    at htsjdk.samtools.seekablestream.SeekableFileStream.read(SeekableFileStream.java:85)
    at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:571)
    at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:560)
    at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:510)
    at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
    at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
    at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
    at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
    at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:257)
    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:333)
    at java.base/sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:376)
    at java.base/sun.nio.cs.StreamDecoder.lockedRead(StreamDecoder.java:219)
    at java.base/sun.nio.cs.StreamDecoder.read(StreamDecoder.java:173)
    at java.base/java.io.InputStreamReader.read(InputStreamReader.java:189)
    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)
    ... 25 more

The strange thing is that the same command has been run to completion on other chromosomes without errors.

Thank you for your help!