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 -Xmx10g -jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar GenotypeGVCFs -R Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa -V SRR.g.vcf -O SRR.vcf.gz
11:50:07.691 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
11:50:07.730 INFO  GenotypeGVCFs - ------------------------------------------------------------
11:50:07.733 INFO  GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.4.0.0
11:50:07.733 INFO  GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
11:50:07.733 INFO  GenotypeGVCFs - Executing as formation@n026 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64
11:50:07.733 INFO  GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.6+9-LTS-190
11:50:07.733 INFO  GenotypeGVCFs - Start Date/Time: November 7, 2023 at 11:50:07 AM CET
11:50:07.733 INFO  GenotypeGVCFs - ------------------------------------------------------------
11:50:07.733 INFO  GenotypeGVCFs - ------------------------------------------------------------
11:50:07.741 INFO  GenotypeGVCFs - HTSJDK Version: 3.0.5
11:50:07.741 INFO  GenotypeGVCFs - Picard Version: 3.0.0
11:50:07.741 INFO  GenotypeGVCFs - Built for Spark Version: 3.3.1
11:50:07.742 INFO  GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:50:07.742 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:50:07.743 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:50:07.743 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:50:07.743 INFO  GenotypeGVCFs - Deflater: IntelDeflater
11:50:07.743 INFO  GenotypeGVCFs - Inflater: IntelInflater
11:50:07.744 INFO  GenotypeGVCFs - GCS max retries/reopens: 20
11:50:07.745 INFO  GenotypeGVCFs - Requester pays: disabled
11:50:07.745 INFO  GenotypeGVCFs - Initializing engine
11:50:07.936 INFO  FeatureManager - Using codec VCFCodec to read file file:///work/user/formation/Formation_Aln-SNP3/SRR.g.vcf
11:50:08.092 INFO  GenotypeGVCFs - Done initializing engine
11:50:08.190 INFO  ProgressMeter - Starting traversal
11:50:08.190 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
11:50:08.459 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 25:71 and possibly subsequent; at least 10 samples must have called genotypes
11:50:18.192 INFO  ProgressMeter -           25:1171828              0.2                236000        1416000.0
11:50:28.192 INFO  ProgressMeter -             26:59556              0.3                927000        2780861.0
11:50:38.195 INFO  ProgressMeter -           26:2932515              0.5               2152000        4303426.2
11:50:45.815 INFO  ProgressMeter -           26:5312069              0.6               3154217        5030381.7
11:50:45.815 INFO  ProgressMeter - Traversal complete. Processed 3154217 total variants in 0.6 minutes.
11:50:45.825 INFO  GenotypeGVCFs - Shutting down engine
[November 7, 2023 at 11:50:45 AM CET] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.64 minutes.
Runtime.totalMemory()=243335168