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 -Xmx7g -jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar BaseRecalibrator -I SRR7062654.md.bam -O SRR7062654.md.recal.table --tmp-dir . -R Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa --known-sites Gallus_gallus_incl_consequences_chr25-26.vcf --verbosity INFO
11:09:32.046 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
11:09:32.127 INFO  BaseRecalibrator - ------------------------------------------------------------
11:09:32.131 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.4.0.0
11:09:32.131 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
11:09:32.131 INFO  BaseRecalibrator - Executing as formation@n024 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64
11:09:32.131 INFO  BaseRecalibrator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.6+9-LTS-190
11:09:32.131 INFO  BaseRecalibrator - Start Date/Time: November 7, 2023 at 11:09:31 AM CET
11:09:32.132 INFO  BaseRecalibrator - ------------------------------------------------------------
11:09:32.132 INFO  BaseRecalibrator - ------------------------------------------------------------
11:09:32.133 INFO  BaseRecalibrator - HTSJDK Version: 3.0.5
11:09:32.147 INFO  BaseRecalibrator - Picard Version: 3.0.0
11:09:32.148 INFO  BaseRecalibrator - Built for Spark Version: 3.3.1
11:09:32.148 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:09:32.149 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:09:32.150 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:09:32.150 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:09:32.150 INFO  BaseRecalibrator - Deflater: IntelDeflater
11:09:32.151 INFO  BaseRecalibrator - Inflater: IntelInflater
11:09:32.151 INFO  BaseRecalibrator - GCS max retries/reopens: 20
11:09:32.151 INFO  BaseRecalibrator - Requester pays: disabled
11:09:32.153 INFO  BaseRecalibrator - Initializing engine
11:09:32.159 INFO  BaseRecalibrator - Shutting down engine
[November 7, 2023 at 11:09:32 AM CET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=162267136
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A USER ERROR has occurred: Fasta dict file file:///work/user/formation/Formation_Aln-SNP3/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.dict for reference file:///work/user/formation/Formation_Aln-SNP3/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.

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