REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

I got this error message when running gatk ApplyBQSR on GATK v4.5.0.0. Could you help me with this?

Thank you,

My code was:

parallel -j 32 "java -XX:ParallelGCThreads=1 \
        -DGATK_STACKTRACE_ON_USER_EXCEPTION=true \
        -jar gatk-package-4.5.0.0-local.jar BaseRecalibrator \
        --input {}.sort.dedup.grp.bam \
        --known-sites ${vcf} \
        --reference ${reference_fasta} \
        --output {}.recal.table \
        2>${log_dir}/{}.recal1.log" ::: $(ls -1 *.sort.dedup.grp.bam | sed 's/.sort.dedup.grp.bam//')

The error message is below.

08:43:36.201 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/user1/Programs/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
08:43:36.410 INFO  ApplyBQSR - ------------------------------------------------------------
08:43:36.414 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.5.0.0
08:43:36.414 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
08:43:36.414 INFO  ApplyBQSR - Executing as user1@agriserver.ca on Linux v5.4.0-150-generic amd64
08:43:36.415 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.3-internal+0-adhoc..src
08:43:36.415 INFO  ApplyBQSR - Start Date/Time: March 26, 2024 at 8:43:36 a.m. CST
08:43:36.416 INFO  ApplyBQSR - ------------------------------------------------------------
08:43:36.416 INFO  ApplyBQSR - ------------------------------------------------------------
08:43:36.417 INFO  ApplyBQSR - HTSJDK Version: 4.1.0
08:43:36.418 INFO  ApplyBQSR - Picard Version: 3.1.1
08:43:36.418 INFO  ApplyBQSR - Built for Spark Version: 3.5.0
08:43:36.418 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
08:43:36.418 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
08:43:36.419 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
08:43:36.419 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
08:43:36.419 INFO  ApplyBQSR - Deflater: IntelDeflater
08:43:36.420 INFO  ApplyBQSR - Inflater: IntelInflater
08:43:36.420 INFO  ApplyBQSR - GCS max retries/reopens: 20
08:43:36.420 INFO  ApplyBQSR - Requester pays: disabled
08:43:36.421 INFO  ApplyBQSR - Initializing engine
08:43:36.612 INFO  ApplyBQSR - Done initializing engine
08:43:36.696 INFO  ProgressMeter - Starting traversal
08:43:36.697 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
08:43:46.706 INFO  ProgressMeter -       Chr1A:23226847              0.2                517000        3100139.9
08:43:56.714 INFO  ProgressMeter -       Chr1A:87627473              0.3               1171000        3510191.8
08:44:06.717 INFO  ProgressMeter -      Chr1A:234195235              0.5               1891000        3779606.2
08:44:16.728 INFO  ProgressMeter -      Chr1A:337380910              0.7               2597000        3892483.3
08:44:26.737 INFO  ProgressMeter -      Chr1A:400141378              0.8               3185000        3818944.8
08:44:36.741 INFO  ProgressMeter -      Chr1A:473780646              1.0               3844000        3841247.1
08:44:46.746 INFO  ProgressMeter -      Chr1A:519760911              1.2               4452000        3813385.1
08:44:51.207 INFO  ApplyBQSR - Shutting down engine

[March 26, 2024 at 8:44:51 a.m. CST] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 1.25 minutes.
Runtime.totalMemory()=1493172224
htsjdk.samtools.SAMException: Exception when processing alignment for BAM index LH00315:84:22HCFMLT3:7:2291:5577:13834 2/2 156b aligned to Chr1A:536879422-536879577.
        at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:141)
        at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:200)
        at htsjdk.samtools.AsyncSAMFileWriter.synchronouslyWrite(AsyncSAMFileWriter.java:36)
        at htsjdk.samtools.AsyncSAMFileWriter.synchronouslyWrite(AsyncSAMFileWriter.java:16)
        at htsjdk.samtools.util.AbstractAsyncWriter$WriterRunnable.run(AbstractAsyncWriter.java:123)
        at java.base/java.lang.Thread.run(Thread.java:833)

Caused by: htsjdk.samtools.SAMException: Exception creating BAM index for record LH00315:84:22HCFMLT3:7:2291:5577:13834 2/2 156b aligned to Chr1A:536879422-536879577.
        at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:132)
        at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:138)
        ... 5 more

Caused by: java.lang.IllegalStateException: Read position too high for BAI bin indexing.
        at htsjdk.samtools.SAMRecord.computeIndexingBin(SAMRecord.java:1705)
        at htsjdk.samtools.BAMIndexer$BAMIndexBuilder$1.getIndexingBin(BAMIndexer.java:250)
        at htsjdk.samtools.BinningIndexBuilder.processFeature(BinningIndexBuilder.java:96)
        at htsjdk.samtools.BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:238)
        at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:130)