My goal is to subset snps from the input file (AA01_rg.g.vcf). Before using the gatk SelectVariants for this purpose, I used the following command to count number of snps in my input file:

grep -v "#" /scratch/vn81649/snapbean/gvcf_new/AA01_rg.g.vcf | wc -l

This command identified 63702926 snps in the input file. 

However, when I used gatk SelectVariants, the output file exhibited no SNPs. 

REQUIRED for all errors and issues:
a) GATK version used:

The Genome Analysis Toolkit (GATK) v4.2.5.0

b) Exact command used:

ref="/scratch/vn81649/snapbean/Ref/ref.fa"
input="/scratch/vn81649/snapbean/gvcf_new/AA01_rg.g.vcf"
output="/scratch/vn81649/snapbean/snps/AA01_rg.snps.vcf"
time gatk SelectVariants -R $ref -V $input --select-type-to-include SNP -O $output

 
c) Entire program log:

13:48:37.648 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/apps/eb/GATK/4.2.5.0-GCCcore-8.3.0-Java-1.8/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Feb 06, 2023 1:48:37 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
13:48:37.829 INFO  SelectVariants - ------------------------------------------------------------
13:48:37.829 INFO  SelectVariants - The Genome Analysis Toolkit (GATK) v4.2.5.0
13:48:37.829 INFO  SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
13:48:37.831 INFO  SelectVariants - Executing as vn81649@c4-11.compute.lan on Linux v3.10.0-1160.36.2.el7.x86_64 amd64
13:48:37.831 INFO  SelectVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_241-b07
13:48:37.831 INFO  SelectVariants - Start Date/Time: February 6, 2023 1:48:37 PM EST
13:48:37.831 INFO  SelectVariants - ------------------------------------------------------------
13:48:37.831 INFO  SelectVariants - ------------------------------------------------------------
13:48:37.831 INFO  SelectVariants - HTSJDK Version: 2.24.1
13:48:37.831 INFO  SelectVariants - Picard Version: 2.25.4
13:48:37.831 INFO  SelectVariants - Built for Spark Version: 2.4.5
13:48:37.832 INFO  SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:48:37.832 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:48:37.832 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:48:37.832 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:48:37.832 INFO  SelectVariants - Deflater: IntelDeflater
13:48:37.832 INFO  SelectVariants - Inflater: IntelInflater
13:48:37.832 INFO  SelectVariants - GCS max retries/reopens: 20
13:48:37.832 INFO  SelectVariants - Requester pays: disabled
13:48:37.832 INFO  SelectVariants - Initializing engine
13:48:38.515 INFO  FeatureManager - Using codec VCFCodec to read file file:///scratch/vn81649/snapbean/gvcf_new/AA01_rg.g.vcf
13:48:39.755 INFO  SelectVariants - Done initializing engine
13:48:39.779 INFO  ProgressMeter - Starting traversal
13:48:39.779 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
13:50:40.186 INFO  ProgressMeter -             unmapped              2.0                     0              0.0
13:50:40.186 INFO  ProgressMeter - Traversal complete. Processed 0 total variants in 2.0 minutes.
13:50:40.188 INFO  SelectVariants - Shutting down engine
[February 6, 2023 1:50:40 PM EST] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 2.04 minutes.
Runtime.totalMemory()=2010120192
Using GATK jar /apps/eb/GATK/4.2.5.0-GCCcore-8.3.0-Java-1.8/gatk-package-4.2.5.0-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 -jar /apps/eb/GATK/4.2.5.0-GCCcore-8.3.0-Java-1.8/gatk-package-4.2.5.0-local.jar SelectVariants -R /scratch/vn81649/snapbean/Ref/ref.fa -V /scratch/vn81649/snapbean/gvcf_new/AA01_rg.g.vcf --select-type-to-include SNP -O /scratch/vn81649/snapbean/snps/AA01_rg.snps.vcf

real    2m6.465s
user    2m5.670s
sys     0m6.761s
end