gVCF ALT Column Showing Only <NON_REF>

[kotchanipar]

I use gatk CombineGVCFs to merge *gvcf files after running Haplotypecaller using command below

gatk CombineGVCFs -R ${ref} -V merge.list -O comnine_all.gvcf.gz

but it has the following warning message

`The following have been reloaded with a version change:

1. GCCcore/11.2.0 => GCCcore/12.2.0

WARNING: GATK v4.1.4.1 support for Java 11 is in beta state. Use at your own risk.

The following have been reloaded with a version change:

1. GATK/4.5.0-java-17 => GATK/4.1.4.1-GCCcore-8.3.0-Java-11
2. GCCcore/12.2.0 => GCCcore/8.3.0
3. GMP/6.2.1-GCCcore-11.2.0 => GMP/6.1.2-GCCcore-8.3.0
4. Java/17.0.4 => Java/11.0.16
5. Python/3.9.6-GCCcore-11.2.0 => Python/3.7.4-GCCcore-8.3.0
6. SQLite/3.36-GCCcore-11.2.0 => SQLite/3.29.0-GCCcore-8.3.0
7. Tcl/8.6.11-GCCcore-11.2.0 => Tcl/8.6.9-GCCcore-8.3.0
8. XZ/5.2.5-GCCcore-11.2.0 => XZ/5.2.4-GCCcore-8.3.0
9. binutils/2.37-GCCcore-11.2.0 => binutils/2.32-GCCcore-8.3.0
10. bzip2/1.0.8-GCCcore-11.2.0 => bzip2/1.0.8-GCCcore-8.3.0
11. libffi/3.4.2-GCCcore-11.2.0 => libffi/3.2.1-GCCcore-8.3.0
12. libreadline/8.1-GCCcore-11.2.0 => libreadline/8.0-GCCcore-8.3.0
13. ncurses/6.2-GCCcore-11.2.0 => ncurses/6.1-GCCcore-8.3.0
14. zlib/1.2.11-GCCcore-11.2.0 => zlib/1.2.11-GCCcore-8.3.0

13:26:41.785 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/nbt_main/share/module_new/modules/software/GATK/4.1.4.1-GCCcore-8.3.0-Java-11/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Sep 09, 2024 1:26:42 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
13:26:42.114 INFO CombineGVCFs - ------------------------------------------------------------
13:26:42.115 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.1.4.1
13:26:42.115 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
13:26:42.115 INFO CombineGVCFs - Executing as [email protected] on Linux v4.18.0-305.el8.x86_64 amd64
13:26:42.115 INFO CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v11.0.16+8
13:26:42.115 INFO CombineGVCFs - Start Date/Time: September 9, 2024 at 1:26:41 PM ICT
13:26:42.115 INFO CombineGVCFs - ------------------------------------------------------------
13:26:42.115 INFO CombineGVCFs - ------------------------------------------------------------
13:26:42.116 INFO CombineGVCFs - HTSJDK Version: 2.21.0
13:26:42.116 INFO CombineGVCFs - Picard Version: 2.21.2
13:26:42.116 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:26:42.116 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:26:42.116 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:26:42.116 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:26:42.116 INFO CombineGVCFs - Deflater: IntelDeflater
13:26:42.116 INFO CombineGVCFs - Inflater: IntelInflater
13:26:42.116 INFO CombineGVCFs - GCS max retries/reopens: 20
13:26:42.116 INFO CombineGVCFs - Requester pays: disabled
13:26:42.116 INFO CombineGVCFs - Initializing engine
13:26:42.404 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam1.gvcf.gz
13:26:42.569 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam2.gvcf.gz
13:26:42.757 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam3.gvcf.gz
13:26:42.891 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam4.gvcf.gz
13:26:43.003 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam5.gvcf.gz
13:26:43.160 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam6.gvcf.gz
13:26:43.246 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam7.gvcf.gz
13:26:43.316 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam8.gvcf.gz
13:26:43.456 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam9.gvcf.gz
13:26:43.527 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam10.gvcf.gz
13:26:43.631 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam11.gvcf.gz
13:26:43.770 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam12.gvcf.gz
13:26:43.858 INFO FeatureManager - Using codec VCFCodec to read file file:///fang/project/results/sam13.gvcf.gz
13:26:44.623 INFO CombineGVCFs - Done initializing engine
13:26:44.681 INFO ProgressMeter - Starting traversal
13:26:44.681 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:26:45.034 WARN ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location NC_080782.1:78723 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
13:26:54.683 INFO ProgressMeter - NC_080782.1:3768890 0.2 571000 3425657.4
13:27:04.683 INFO ProgressMeter - NC_080782.1:17827068 0.3 1391000 4172791.4
13:27:14.694 INFO ProgressMeter - NC_080782.1:44855178 0.5 2086000 4170192.9
13:27:24.706 INFO ProgressMeter - NC_080782.1:67560924 0.7 2761000 4138913.2
13:27:34.715 INFO ProgressMeter - NC_080782.1:106975576 0.8 3384000 4058121.6`

and the result shows that all entries in the ALT column are <NON_REF>.

Could you help me figure out this problem?