a) GATK version used: GATK 4

b) Exact command used: gatk HaplotypeCaller -R $(GENOME_file_LAB) -I $(FILE).ao.sort.bam -O $(FILE).raw_variants_help.vcf; \

Hi, I would love to help.

I ran the GATK SNP pipeline several times and it worked great!
Now I started running it again, and when I got to HaplotypeCaller it throws me the comment: WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1: 40 and possibly subsequent; at least 10 samples must have called genotypes.

So far I have not received this comment.
In addition, it takes him much longer to output output from previous times.

I suspect it has to do with the genome reference but I do not find the problem ..
Can be?

I did not find a comment in the forum that fits this problem.

Would appreciate help!

Thank you,
Dina

My output:

Using GATK jar /usr/local/hurcs/miniconda3/envs/gatk4-4.2.3.0/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-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 /usr/local/hurcs/miniconda3/envs/gatk4-4.2.3.0/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar HaplotypeCaller -R zv11.fa -I finalBamFilem.bam.ao.sort.bam -O finalBamFilem.bam.raw_variants_help.vcf
15:37:50.110 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/hurcs/miniconda3/envs/gatk4-4.2.3.0/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Mar 13, 2022 3:37:50 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
15:37:50.420 INFO  HaplotypeCaller - ------------------------------------------------------------
15:37:50.421 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.3.0
15:37:50.421 INFO  HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
15:37:50.423 INFO  HaplotypeCaller - Executing as dinnatzur12@glacier-09.cs.huji.ac.il on Linux v5.10.104-aufs-2 amd64
15:37:50.423 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_302-b08
15:37:50.423 INFO  HaplotypeCaller - Start Date/Time: March 13, 2022 3:37:50 PM IST
15:37:50.423 INFO  HaplotypeCaller - ------------------------------------------------------------
15:37:50.424 INFO  HaplotypeCaller - ------------------------------------------------------------
15:37:50.424 INFO  HaplotypeCaller - HTSJDK Version: 2.24.1
15:37:50.424 INFO  HaplotypeCaller - Picard Version: 2.25.4
15:37:50.424 INFO  HaplotypeCaller - Built for Spark Version: 2.4.5
15:37:50.424 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:37:50.424 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:37:50.424 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:37:50.424 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:37:50.425 INFO  HaplotypeCaller - Deflater: IntelDeflater
15:37:50.425 INFO  HaplotypeCaller - Inflater: IntelInflater
15:37:50.425 INFO  HaplotypeCaller - GCS max retries/reopens: 20
15:37:50.425 INFO  HaplotypeCaller - Requester pays: disabled
15:37:50.425 INFO  HaplotypeCaller - Initializing engine
15:37:51.514 INFO  HaplotypeCaller - Done initializing engine
15:37:51.593 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
15:37:51.626 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/usr/local/hurcs/miniconda3/envs/gatk4-4.2.3.0/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_utils.so

15:37:51.660 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/usr/local/hurcs/miniconda3/envs/gatk4-4.2.3.0/share/gatk4-4.2.3.0-0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
15:37:51.688 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
15:37:51.689 INFO  IntelPairHmm - Available threads: 1
15:37:51.689 INFO  IntelPairHmm - Requested threads: 4
15:37:51.689 WARN  IntelPairHmm - Using 1 available threads, but 4 were requested
15:37:51.693 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
15:37:51.821 INFO  ProgressMeter - Starting traversal
15:37:51.822 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
15:37:54.339 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position chr1:40 and possibly subsequent; at least 10 samples must have called genotypes
15:38:27.170 INFO  ProgressMeter -            chr1:6822              0.6                    60            101.8
15:38:57.909 INFO  ProgressMeter -           chr1:10141              1.1                    90             81.7
15:39:09.111 INFO  ProgressMeter -           chr1:15011              1.3                   130            100.9
15:39:22.448 INFO  ProgressMeter -           chr1:32193              1.5                   260            172.1
15:39:34.689 INFO  ProgressMeter -           chr1:42038              1.7                   330            192.5
15:39:45.998 INFO  ProgressMeter -           chr1:70492              1.9                   530            278.5
15:40:00.182 INFO  ProgressMeter -          chr1:153081              2.1                   980            458.1
15:40:15.259 INFO  ProgressMeter -          chr1:154306              2.4                   990            414.1

etc.