Hi,

When I am trying to do the BQSR and VQSR, both has  the same error message:

The commands for BQSR:

java -jar $gatk BaseRecalibrator \
-R ./Homo_sapiens_assembly38.fasta \
-I ./germline_analysis/germline_markdups.bam \
--known-sites Homo_sapiens_assembly38.dbsnp138.vcf \
-O ./germline_analysis/recal_data.table

The commmands for VQSR:

java -jar $gatk VariantRecalibrator 
-R ./data/germline/ref/ref.fasta \
-V ./germline_analysis/trio_jointcalls_hc.vcf.gz \
--resource:hapmap,known=false,training=true,truth=true,prior=15.0 \
 ./hapmap_3.3.hg38.vcf 
--resource:1000G,known=false,training=true,truth=false,prior=12.0 \
 ./1000G_omni2.5.hg38.vcf.gz \
--resource:1000G,known=false,training=true,truth=false,prior=10.0 \
./high_confidence.hg38.vcf.gz \
--resource:dbsnp,known=true,training=false,truth=false,prior=2.0 \
./Homo_sapiens_assembly38.dbsnp138.vcf \
-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP \
-O ./germline_analysis/output.recal 
--tranches-file ./germline_analysis/output.tranches 

The error message is

12:40:31.578 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/jingchun/gatk-4.2.2.0/gatk-package-4.2.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 14, 2021 12:40:32 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
12:40:32.466 INFO VariantRecalibrator - ------------------------------------------------------------
12:40:32.467 INFO VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.2.0
12:40:32.467 INFO VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
12:40:32.472 INFO VariantRecalibrator - Executing as jingchun@jingchun-VirtualBox on Linux v5.11.0-41-generic amd64
12:40:32.473 INFO VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.1+12-Ubuntu-120.04
12:40:32.478 INFO VariantRecalibrator - Start Date/Time: December 14, 2021 at 12:40:31 PM EST
12:40:32.478 INFO VariantRecalibrator - ------------------------------------------------------------
12:40:32.479 INFO VariantRecalibrator - ------------------------------------------------------------
12:40:32.480 INFO VariantRecalibrator - HTSJDK Version: 2.24.1
12:40:32.480 INFO VariantRecalibrator - Picard Version: 2.25.4
12:40:32.481 INFO VariantRecalibrator - Built for Spark Version: 2.4.5
12:40:32.481 INFO VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:40:32.481 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:40:32.482 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:40:32.482 INFO VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:40:32.482 INFO VariantRecalibrator - Deflater: IntelDeflater
12:40:32.482 INFO VariantRecalibrator - Inflater: IntelInflater
12:40:32.484 INFO VariantRecalibrator - GCS max retries/reopens: 20
12:40:32.487 INFO VariantRecalibrator - Requester pays: disabled
12:40:32.488 INFO VariantRecalibrator - Initializing engine
12:40:33.017 INFO FeatureManager - Using codec VCFCodec to read file file:///home/jingchun/GATK/./hapmap_3.3.hg38.vcf
12:40:33.271 INFO FeatureManager - Using codec VCFCodec to read file file:///home/jingchun/GATK/./1000G_omni2.5.hg38.vcf.gz
12:40:33.938 INFO FeatureManager - Using codec VCFCodec to read file file:///home/jingchun/GATK/./high_confidence.hg38.vcf.gz
12:40:34.717 INFO FeatureManager - Using codec VCFCodec to read file file:///home/jingchun/GATK/./Homo_sapiens_assembly38.dbsnp138.vcf
12:40:34.882 INFO FeatureManager - Using codec VCFCodec to read file file:///home/jingchun/GATK/./germline_analysis/trio_jointcalls_hc.vcf.gz
12:40:34.920 WARN IntelInflater - Zero Bytes Written : 0
12:40:34.937 WARN IntelInflater - Zero Bytes Written : 0
12:40:38.909 INFO VariantRecalibrator - Shutting down engine
[December 14, 2021 at 12:40:38 PM EST] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=248512512
***********************************************************************

A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.
reference contigs = [20]

I guess both are due to the resource sequences. I downloaded these sequences from

'genomics-public-data/resources/broad/hg38/v0'.

I want to know which sequences I should use. Another question is why it has this error so I can understand the problem better.

Thanks,

Jingchun

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.2.2.0
b) Exact command used:
c) Entire error log: