Using GATK jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-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 -Xmx14g -jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar ApplyBQSR -R Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa --input SRR7062654.md.bam --output SRR7062654.md.recal.bam --bqsr-recal-file SRR7062654.md.recal.table
11:12:38.509 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
11:12:38.563 INFO  ApplyBQSR - ------------------------------------------------------------
11:12:38.565 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.4.0.0
11:12:38.566 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
11:12:38.566 INFO  ApplyBQSR - Executing as formation@n002 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64
11:12:38.566 INFO  ApplyBQSR - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.6+9-LTS-190
11:12:38.579 INFO  ApplyBQSR - Start Date/Time: November 7, 2023 at 11:12:38 AM CET
11:12:38.579 INFO  ApplyBQSR - ------------------------------------------------------------
11:12:38.579 INFO  ApplyBQSR - ------------------------------------------------------------
11:12:38.580 INFO  ApplyBQSR - HTSJDK Version: 3.0.5
11:12:38.580 INFO  ApplyBQSR - Picard Version: 3.0.0
11:12:38.581 INFO  ApplyBQSR - Built for Spark Version: 3.3.1
11:12:38.581 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:12:38.582 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:12:38.582 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:12:38.583 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:12:38.583 INFO  ApplyBQSR - Deflater: IntelDeflater
11:12:38.583 INFO  ApplyBQSR - Inflater: IntelInflater
11:12:38.584 INFO  ApplyBQSR - GCS max retries/reopens: 20
11:12:38.584 INFO  ApplyBQSR - Requester pays: disabled
11:12:38.585 INFO  ApplyBQSR - Initializing engine
11:12:38.753 INFO  ApplyBQSR - Done initializing engine
11:12:38.767 INFO  ProgressMeter - Starting traversal
11:12:38.768 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
11:12:48.779 INFO  ProgressMeter -           25:2250230              0.2                376000        2254872.6
11:12:58.795 INFO  ProgressMeter -           26:2181630              0.3               1079000        3234250.9
11:13:08.793 INFO  ProgressMeter -           26:4588744              0.5               1794000        3585131.9
11:13:11.624 WARN  IntelInflater - Zero Bytes Written : 0
11:13:11.632 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

11:13:11.633 INFO  ProgressMeter -           26:5311530              0.5               1988606        3630499.3
11:13:11.633 INFO  ProgressMeter - Traversal complete. Processed 1988606 total reads in 0.5 minutes.
11:13:11.684 INFO  ApplyBQSR - Shutting down engine
[November 7, 2023 at 11:13:11 AM CET] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.55 minutes.
Runtime.totalMemory()=243335168