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 SRR7062655.md.bam --output SRR7062655.md.recal.bam --bqsr-recal-file SRR7062655.md.recal.table
11:12:39.374 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
11:12:39.408 INFO  ApplyBQSR - ------------------------------------------------------------
11:12:39.410 INFO  ApplyBQSR - The Genome Analysis Toolkit (GATK) v4.4.0.0
11:12:39.410 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
11:12:39.410 INFO  ApplyBQSR - Executing as formation@n024 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64
11:12:39.410 INFO  ApplyBQSR - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.6+9-LTS-190
11:12:39.411 INFO  ApplyBQSR - Start Date/Time: November 7, 2023 at 11:12:39 AM CET
11:12:39.411 INFO  ApplyBQSR - ------------------------------------------------------------
11:12:39.411 INFO  ApplyBQSR - ------------------------------------------------------------
11:12:39.412 INFO  ApplyBQSR - HTSJDK Version: 3.0.5
11:12:39.412 INFO  ApplyBQSR - Picard Version: 3.0.0
11:12:39.413 INFO  ApplyBQSR - Built for Spark Version: 3.3.1
11:12:39.413 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:12:39.413 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:12:39.414 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:12:39.414 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:12:39.414 INFO  ApplyBQSR - Deflater: IntelDeflater
11:12:39.414 INFO  ApplyBQSR - Inflater: IntelInflater
11:12:39.415 INFO  ApplyBQSR - GCS max retries/reopens: 20
11:12:39.415 INFO  ApplyBQSR - Requester pays: disabled
11:12:39.416 INFO  ApplyBQSR - Initializing engine
11:12:39.695 INFO  ApplyBQSR - Done initializing engine
11:12:39.741 INFO  ProgressMeter - Starting traversal
11:12:39.742 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
11:12:49.760 INFO  ProgressMeter -           25:1128114              0.2                139000         833000.4
11:12:59.767 INFO  ProgressMeter -            26:690216              0.3                674000        2020181.8
11:13:09.773 INFO  ProgressMeter -           26:3337625              0.5               1372000        2741258.7
11:13:19.788 INFO  ProgressMeter -           26:5152152              0.7               1882000        2820039.0
11:13:20.538 WARN  IntelInflater - Zero Bytes Written : 0
11:13:20.542 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

11:13:20.543 INFO  ProgressMeter -           26:5311728              0.7               1921919        2826351.5
11:13:20.544 INFO  ProgressMeter - Traversal complete. Processed 1921919 total reads in 0.7 minutes.
11:13:20.594 INFO  ApplyBQSR - Shutting down engine
[November 7, 2023 at 11:13:20 AM CET] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.69 minutes.
Runtime.totalMemory()=243335168