CNNScoreVariants - GATK 4.5.0.0 error

Question

[dophuochuy94]

/home/thang/huy/tools/gatk/gatk CNNScoreVariants \
  -V 24WES042_20240424-971-2104_WES-11_I.haplo.vcf \
  -R /home/thang/huy/ref/GRCh38.fa \
  -O 24WES042_20240424-971-2104_WES-11_I.annotated.vcf

I already ran conda activate gatk

My GATK version 4.5.0.0, Java 17.

Error as below

Using GATK jar /home/thang/huy/tools/gatk/build/libs/gatk-package-4.5.0.0-40-g948cd4f-SNAPSHOT-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 /home/thang/huy/tools/gatk/build/libs/gatk-package-4.5.0.0-40-g948cd4f-SNAPSHOT-local.jar CNNScoreVariants -V 24WES042_20240424-971-2104_WES-11_I.haplo.vcf -R /home/thang/huy/ref/GRCh38.fa -O 24WES042_20240424-971-2104_WES-11_I.annotated.vcf
09:18:10.451 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/thang/huy/tools/gatk/build/libs/gatk-package-4.5.0.0-40-g948cd4f-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
09:18:10.604 INFO  CNNScoreVariants - ------------------------------------------------------------
09:18:10.606 INFO  CNNScoreVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0-40-g948cd4f-SNAPSHOT
09:18:10.606 INFO  CNNScoreVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
09:18:10.606 INFO  CNNScoreVariants - Executing as thang@thang-WS on Linux v5.15.0-73-generic amd64
09:18:10.606 INFO  CNNScoreVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.11+9-Ubuntu-120.04.2
09:18:10.607 INFO  CNNScoreVariants - Start Date/Time: June 25, 2024 at 9:18:10 AM CDT
09:18:10.607 INFO  CNNScoreVariants - ------------------------------------------------------------
09:18:10.607 INFO  CNNScoreVariants - ------------------------------------------------------------
09:18:10.607 INFO  CNNScoreVariants - HTSJDK Version: 4.1.0
09:18:10.607 INFO  CNNScoreVariants - Picard Version: 3.1.1
09:18:10.607 INFO  CNNScoreVariants - Built for Spark Version: 3.5.0
09:18:10.607 INFO  CNNScoreVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:18:10.608 INFO  CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:18:10.608 INFO  CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:18:10.608 INFO  CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:18:10.608 INFO  CNNScoreVariants - Deflater: IntelDeflater
09:18:10.608 INFO  CNNScoreVariants - Inflater: IntelInflater
09:18:10.608 INFO  CNNScoreVariants - GCS max retries/reopens: 20
09:18:10.608 INFO  CNNScoreVariants - Requester pays: disabled
09:18:10.608 INFO  CNNScoreVariants - Initializing engine
09:18:10.705 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/thang/huy/wesdata/24WES/24WES042_20240424-971-2104_WES-11_I.haplo.vcf
09:18:10.765 INFO  CNNScoreVariants - Done initializing engine
09:18:10.766 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/thang/huy/tools/gatk/build/libs/gatk-package-4.5.0.0-40-g948cd4f-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_utils.so
09:18:11.965 INFO  CNNScoreVariants - Done scoring variants with CNN.
09:18:11.965 INFO  CNNScoreVariants - Shutting down engine
[June 25, 2024 at 9:18:11 AM CDT] org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=629145600
java.lang.IllegalArgumentException: Resource not found: large/cnn_score_variants/1d_cnn_mix_train_full_bn.json
    at org.broadinstitute.hellbender.utils.io.Resource.getResourceContentsAsStream(Resource.java:65)
    at org.broadinstitute.hellbender.utils.io.IOUtils.writeResource(IOUtils.java:213)
    at org.broadinstitute.hellbender.utils.io.IOUtils.writeTempResource(IOUtils.java:185)
    at org.broadinstitute.hellbender.utils.io.IOUtils.writeTempResourceFromPath(IOUtils.java:201)
    at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.initializePythonArgsAndModel(CNNScoreVariants.java:544)
    at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.onTraversalStart(CNNScoreVariants.java:319)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1096)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
    at org.broadinstitute.hellbender.Main.main(Main.java:306)