REQUIRED for all errors and issues:
a) GATK version used: gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar

b) Exact command used:gatk BaseRecalibrator -I ${aligned_reads}/SRR062634_sorted_dedup_reads.bam -R ${ref} --known-sites ${known_sites} -O ${data}/recal_data.table

gatk ApplyBQSR -I ${aligned_reads}/SRR062634_sorted_dedup_reads.bam -R ${ref} --bqsr-recal-file {$data}/recal_data.table -O ${aligned_reads}/SRR062634_sorted_dedup_bqsr_reads.bam 

c) Entire program log:

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/aaina/apps/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar ApplyBQSR -I /home/aaina/Desktop/demo/VC/aligned_reads/SRR062634_sorted_dedup_reads.bam -R /home/aaina/Desktop/demo/supporting_files/hg38/hg38.fa --bqsr-recal-file {/home/aaina/Desktop/demo/VC/data}/recal_data.table -O /home/aaina/Desktop/demo/VC/aligned_reads/SRR062634_sorted_dedup_bqsr_reads.bam

13:44:51.895 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/aaina/apps/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

13:44:51.989 INFO  ApplyBQSR - ------------------------------------------------------------

13:44:51.991 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.5.0.0

13:44:51.992 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/

13:44:51.992 INFO  ApplyBQSR - Executing as aaina@ellison on Linux v4.18.0-513.11.1.el8_9.x86_64 amd64

13:44:51.992 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v22+36-2370

13:44:51.992 INFO  ApplyBQSR - Start Date/Time: May 16, 2024, 1:44:51 PM CDT

13:44:51.992 INFO  ApplyBQSR - ------------------------------------------------------------

13:44:51.992 INFO  ApplyBQSR - ------------------------------------------------------------

13:44:51.993 INFO  ApplyBQSR - HTSJDK Version: 4.1.0

13:44:51.993 INFO  ApplyBQSR - Picard Version: 3.1.1

13:44:51.993 INFO  ApplyBQSR - Built for Spark Version: 3.5.0

13:44:51.993 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2

13:44:51.993 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

13:44:51.993 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

13:44:51.993 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

13:44:51.993 INFO  ApplyBQSR - Deflater: IntelDeflater

13:44:51.993 INFO  ApplyBQSR - Inflater: IntelInflater

13:44:51.994 INFO  ApplyBQSR - GCS max retries/reopens: 20

13:44:51.994 INFO  ApplyBQSR - Requester pays: disabled

13:44:51.994 INFO  ApplyBQSR - Initializing engine

13:44:52.121 INFO  ApplyBQSR - Done initializing engine

13:44:52.137 INFO  ProgressMeter - Starting traversal

13:44:52.138 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute

13:44:52.214 INFO  ApplyBQSR - Shutting down engine

[May 16, 2024, 1:44:52 PM CDT] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.01 minutes.

Runtime.totalMemory()=1140850688

***********************************************************************

A USER ERROR has occurred: Couldn't read file. Error was: {/home/aaina/Desktop/demo/VC/data}/recal_data.table with exception: {/home/aaina/Desktop/demo/VC/data}/recal_data.table (No such file or directory)

***********************************************************************

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.