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 CombineGVCFs -R Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa -O SRR.g.vcf --variant SRR7062654.md.recal.g.vcf --variant SRR7062655.md.recal.g.vcf
11:48:39.922 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
11:48:39.967 INFO  CombineGVCFs - ------------------------------------------------------------
11:48:39.969 INFO  CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.4.0.0
11:48:39.970 INFO  CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
11:48:39.970 INFO  CombineGVCFs - Executing as formation@n026 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64
11:48:39.970 INFO  CombineGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.6+9-LTS-190
11:48:39.970 INFO  CombineGVCFs - Start Date/Time: November 7, 2023 at 11:48:39 AM CET
11:48:39.970 INFO  CombineGVCFs - ------------------------------------------------------------
11:48:39.970 INFO  CombineGVCFs - ------------------------------------------------------------
11:48:39.971 INFO  CombineGVCFs - HTSJDK Version: 3.0.5
11:48:39.971 INFO  CombineGVCFs - Picard Version: 3.0.0
11:48:39.972 INFO  CombineGVCFs - Built for Spark Version: 3.3.1
11:48:39.972 INFO  CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:48:39.973 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:48:39.973 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:48:39.973 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:48:39.974 INFO  CombineGVCFs - Deflater: IntelDeflater
11:48:39.974 INFO  CombineGVCFs - Inflater: IntelInflater
11:48:39.975 INFO  CombineGVCFs - GCS max retries/reopens: 20
11:48:39.975 INFO  CombineGVCFs - Requester pays: disabled
11:48:39.976 INFO  CombineGVCFs - Initializing engine
11:48:40.195 INFO  FeatureManager - Using codec VCFCodec to read file file:///work/user/formation/Formation_Aln-SNP3/SRR7062654.md.recal.g.vcf
11:48:40.279 INFO  FeatureManager - Using codec VCFCodec to read file file:///work/user/formation/Formation_Aln-SNP3/SRR7062655.md.recal.g.vcf
11:48:40.435 INFO  CombineGVCFs - Done initializing engine
11:48:40.460 INFO  ProgressMeter - Starting traversal
11:48:40.460 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
11:48:40.591 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 25:71 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
11:48:50.485 INFO  ProgressMeter -           25:1304596              0.2                336000        2013382.6
11:49:00.476 INFO  ProgressMeter -            26:265870              0.3               1187000        3558153.5
11:49:10.488 INFO  ProgressMeter -           26:2996879              0.5               2577000        5150223.2
11:49:18.517 INFO  ProgressMeter -           26:5312755              0.6               3720084        5865019.3
11:49:18.518 INFO  ProgressMeter - Traversal complete. Processed 3720084 total variants in 0.6 minutes.
11:49:18.600 INFO  CombineGVCFs - Shutting down engine
[November 7, 2023 at 11:49:18 AM CET] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.65 minutes.
Runtime.totalMemory()=243335168