In recalibrating base quality scores step, I am trying to create a calibration table using BaseRecalibrator tool of GATK. Firstly, I have generated fai file by samtools faidx and dictionary by GATK CreateSequenceDictionary from the reference genome hg38.fa.

However, when I run the BaseCalibrator it says java.lang.IllegalArgumentException: Something went wrong with sequence dictionary detection, check that reference has a valid sequence dictionary. To be more specific, I get this:

17:01:16.440 WARN  NativeLibraryLoader - Unable to find native library: native/gkl_compression.dll
17:01:16.448 WARN  NativeLibraryLoader - Unable to find native library: native/gkl_compression.dll
17:01:16.558 INFO  BaseRecalibrator - ------------------------------------------------------------
17:01:16.559 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.6.1
17:01:16.560 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:01:16.563 INFO  BaseRecalibrator - Executing as Arda@DESKTOP-SVMGMAP on Windows 10 v10.0 x86
17:01:16.564 INFO  BaseRecalibrator - Java runtime: Java HotSpot(TM) Client VM v1.8.0_341-b10
17:01:16.564 INFO  BaseRecalibrator - Start Date/Time: 09 A­ustos 2022 Sal² 17:01:16 EET
17:01:16.565 INFO  BaseRecalibrator - ------------------------------------------------------------
17:01:16.566 INFO  BaseRecalibrator - ------------------------------------------------------------
17:01:16.567 INFO  BaseRecalibrator - HTSJDK Version: 2.24.1
17:01:16.567 INFO  BaseRecalibrator - Picard Version: 2.27.1
17:01:16.568 INFO  BaseRecalibrator - Built for Spark Version: 2.4.5
17:01:16.568 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:01:16.569 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:01:16.569 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:01:16.570 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:01:16.570 INFO  BaseRecalibrator - Deflater: JdkDeflater
17:01:16.571 INFO  BaseRecalibrator - Inflater: JdkInflater
17:01:16.573 INFO  BaseRecalibrator - GCS max retries/reopens: 20
17:01:16.574 INFO  BaseRecalibrator - Requester pays: disabled
17:01:16.576 INFO  BaseRecalibrator - Initializing engine
17:01:16.638 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:01:16.643 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:01:17.278 INFO  FeatureManager - Using codec VCFCodec to read file file:///D:/--/gatk-4.2.6.1/known-sites/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf
17:01:17.322 INFO  FeatureManager - Using codec VCFCodec to read file file:///D:/--/gatk-4.2.6.1/known-sites/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf
17:01:17.383 INFO  FeatureManager - Using codec VCFCodec to read file file:///D:/--/gatk-4.2.6.1/known-sites/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf
17:01:17.442 INFO  BaseRecalibrator - Shutting down engine
[09 Ağustos 2022 Salı 17:01:17 EET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=34865152
java.lang.IllegalArgumentException: Something went wrong with sequence dictionary detection, check that reference has a valid sequence dictionary
        at org.broadinstitute.hellbender.utils.Utils.nonNull(Utils.java:643)
        at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:149)
        at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:98)
        at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(GATKTool.java:796)
        at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:731)
        at org.broadinstitute.hellbender.engine.ReadWalker.onStartup(ReadWalker.java:51)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)

I thought something might be wrong with dictionary file and realized it only includes this line:

@HD VN:1.6

I don't think this is what it should look like. Repeating the generating dict file yielded the same output. Now, I am not sure if I should really use hg38.fa as reference. Because the lack of documentation, there is no clear statements regarding to choice of reference. I couldn't sort out what's the wrong with my code.

If it's required, this is what I run:

java -jar gatk-package-4.2.6.1-local.jar BaseRecalibrator -I data/markdup1.bam -R ref/hg38.fa --known-sites known-sites/resources_broad_hg38_v0_1000G_phase1.snps.high_confidence.hg38.vcf --known-sites known-sites/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf --known-sites known-sites/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf -O data/recal_data1.table