Running tool:CNNVariantWriteTensors did not produce any files.

[sujianed]

########code: docker run -it -v /media/sj/14t1:/data2 broadinstitute/gatk:latest

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 /gatk/gatk-package-4.4.0.0-local.jar CNNVariantWriteTensors --output-tensor-dir /data2/example/results --reference /data2/example/1/hg19.fa --truth-bed /data2/example/hg19.hybrid.bed --truth-vcf /data2/example/hg19.hybrid.vcf.gz --variant /data2/example/NA12877.vcf.gz

##########result: 02:02:31.316 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 02:02:31.342 INFO CNNVariantWriteTensors - ------------------------------------------------------------ 02:02:31.345 INFO CNNVariantWriteTensors - The Genome Analysis Toolkit (GATK) v4.4.0.0 02:02:31.345 INFO CNNVariantWriteTensors - For support and documentation go to https://software.broadinstitute.org/gatk/ 02:02:31.345 INFO CNNVariantWriteTensors - Executing as root@d768be9a3fc5 on Linux v5.15.0-79-generic amd64 02:02:31.345 INFO CNNVariantWriteTensors - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10-Ubuntu-0ubuntu118.04.1 02:02:31.345 INFO CNNVariantWriteTensors - Start Date/Time: August 30, 2023 at 2:02:31 AM GMT 02:02:31.345 INFO CNNVariantWriteTensors - ------------------------------------------------------------ 02:02:31.345 INFO CNNVariantWriteTensors - ------------------------------------------------------------ 02:02:31.346 INFO CNNVariantWriteTensors - HTSJDK Version: 3.0.5 02:02:31.346 INFO CNNVariantWriteTensors - Picard Version: 3.0.0 02:02:31.346 INFO CNNVariantWriteTensors - Built for Spark Version: 3.3.1 02:02:31.346 INFO CNNVariantWriteTensors - HTSJDK Defaults.COMPRESSION_LEVEL : 2 02:02:31.346 INFO CNNVariantWriteTensors - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 02:02:31.346 INFO CNNVariantWriteTensors - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 02:02:31.347 INFO CNNVariantWriteTensors - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 02:02:31.347 INFO CNNVariantWriteTensors - Deflater: IntelDeflater 02:02:31.347 INFO CNNVariantWriteTensors - Inflater: IntelInflater 02:02:31.347 INFO CNNVariantWriteTensors - GCS max retries/reopens: 20 02:02:31.347 INFO CNNVariantWriteTensors - Requester pays: disabled 02:02:31.347 WARN CNNVariantWriteTensors -

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Warning: CNNVariantWriteTensors is an EXPERIMENTAL tool and should not be used for production

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02:02:31.347 INFO CNNVariantWriteTensors - Initializing engine 02:02:33.899 INFO CNNVariantWriteTensors - Done initializing engine 02:02:33.899 INFO CNNVariantWriteTensors - Args are:[--reference_fasta, /data2/example/1/hg19.fa, --input_vcf, /data2/example/NA12877.vcf.gz, --bam_file, , --train_vcf, /data2/example/hg19.hybrid.vcf.gz, --bed_file, /data2/example/hg19.hybrid.bed, --tensor_name, reference, --annotation_set, best_practices, --samples, 1000000, --downsample_snps, 0.05, --downsample_indels, 0.5, --data_dir, /data2/example/results, --channels_last, --mode, write_reference_and_annotation_tensors] 02:38:41.806 INFO CNNVariantWriteTensors - Shutting down engine [August 30, 2023 at 2:38:41 AM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.CNNVariantWriteTensors done. Elapsed time: 36.18 minutes. Runtime.totalMemory()=285212672 Tool returned: true

####issue: /data2/example/results is empty, and no file was generated.