Hi GATK team,

I tried running the following command, however it throws the listed error. I suspect it's because of the underscores in the google bucket name, however just wanted to confirm if GATK has had previously known issues like this.

a) GATK version used:

The Genome Analysis Toolkit (GATK) v4.2.6.1

 
b) Exact command used:

gatk --java-options "-Xms63g -XX:+UseParallelGC -XX:ParallelGCThreads=3" \
          VariantRecalibrator \
          -V gs://daly_schema2_gnomad_subset_vds/rye-test/outputs/subset_50_2000-vqsr-ready.vcf.bgz \
          -O ${BATCH_TMPDIR}/VQSR__SNPsVariantRecalibratorScattered-CkEY1/recalibration \
          --tranches-file ${BATCH_TMPDIR}/VQSR__SNPsVariantRecalibratorScattered-CkEY1/tranches \
          --trust-all-polymorphic \
          -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.8 -tranche 99.6 -tranche 99.5 -tranche 99.4 -tranche 99.3 -tranche 99.0 -tranche 98.0 -tranche 97.0 -tranche 90.0 \
          -an AS_QD -an AS_MQRankSum -an AS_ReadPosRankSum -an AS_FS -an AS_MQ \
          -mode SNP \
          --max-gaussians 6 \
          -resource:hapmap,known=false,training=true,truth=true,prior=15 gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz \
          -resource:omni,known=false,training=true,truth=true,prior=12 gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz \
          -resource:1000G,known=false,training=true,truth=false,prior=10 gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
          -resource:dbsnp,known=true,training=false,truth=false,prior=7 gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.gz \
         --use-allele-specific-annotations

 
c) Entire program log:

15:55:52.774 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
15:55:52.797 INFO  VariantRecalibrator - ------------------------------------------------------------
15:55:52.798 INFO  VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.6.1
15:55:52.798 INFO  VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:55:52.798 INFO  VariantRecalibrator - Executing as root@hostname-8809556844 on Linux v5.4.0-1042-gcp amd64
15:55:52.798 INFO  VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
15:55:52.798 INFO  VariantRecalibrator - Start Date/Time: November 21, 2022 3:55:52 PM GMT
15:55:52.798 INFO  VariantRecalibrator - ------------------------------------------------------------
15:55:52.798 INFO  VariantRecalibrator - ------------------------------------------------------------
15:55:52.798 INFO  VariantRecalibrator - HTSJDK Version: 2.24.1
15:55:52.799 INFO  VariantRecalibrator - Picard Version: 2.27.1
15:55:52.799 INFO  VariantRecalibrator - Built for Spark Version: 2.4.5
15:55:52.799 INFO  VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:55:52.799 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:55:52.799 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:55:52.799 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:55:52.799 INFO  VariantRecalibrator - Deflater: IntelDeflater
15:55:52.799 INFO  VariantRecalibrator - Inflater: IntelInflater
15:55:52.799 INFO  VariantRecalibrator - GCS max retries/reopens: 20
15:55:52.799 INFO  VariantRecalibrator - Requester pays: disabled
15:55:52.799 INFO  VariantRecalibrator - Initializing engine
15:55:54.309 INFO  FeatureManager - Using codec VCFCodec to read file gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz
15:55:56.132 INFO  FeatureManager - Using codec VCFCodec to read file gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz
15:55:58.182 INFO  FeatureManager - Using codec VCFCodec to read file gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz
15:56:00.610 INFO  FeatureManager - Using codec VCFCodec to read file gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.gz
15:56:02.051 INFO  VariantRecalibrator - Shutting down engine
[November 21, 2022 3:56:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=64827162624
Exception in thread "main" java.lang.AssertionError: java.net.URISyntaxException: Illegal character in hostname at index 9: gs://daly_schema2_gnomad_subset_vds/rye-test/outputs/subset_50_2000-vqsr-ready.vcf.bgz
	at com.google.cloud.storage.contrib.nio.CloudStoragePath.toUri(CloudStoragePath.java:374)
	at org.broadinstitute.hellbender.exceptions.UserException$CouldNotReadInputFile.<init>(UserException.java:79)
	at org.broadinstitute.hellbender.utils.io.IOUtils.assertFileIsReadable(IOUtils.java:857)
	at org.broadinstitute.hellbender.engine.FeatureDataSource.getCodecForFeatureInput(FeatureDataSource.java:396)
	at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:373)
	at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:319)
	at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:291)
	at org.broadinstitute.hellbender.engine.FeatureManager.addToFeatureSources(FeatureManager.java:225)
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$initializeDrivingVariants$0(MultiVariantWalker.java:86)
	at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
	at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:647)
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.initializeDrivingVariants(MultiVariantWalker.java:76)
	at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:67)
	at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:726)
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.onStartup(MultiVariantWalker.java:49)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.net.URISyntaxException: Illegal character in hostname at index 9: gs://daly_schema2_gnomad_subset_vds/rye-test/outputs/subset_50_2000-vqsr-ready.vcf.bgz
	at java.net.URI$Parser.fail(URI.java:2848)
	at java.net.URI$Parser.parseHostname(URI.java:3387)
	at java.net.URI$Parser.parseServer(URI.java:3236)
	at java.net.URI$Parser.parseAuthority(URI.java:3155)
	at java.net.URI$Parser.parseHierarchical(URI.java:3097)
	at java.net.URI$Parser.parse(URI.java:3053)
	at java.net.URI.<init>(URI.java:673)
	at java.net.URI.<init>(URI.java:774)
	at com.google.cloud.storage.contrib.nio.CloudStoragePath.toUri(CloudStoragePath.java:372)
	... 20 more
Using GATK jar /gatk/gatk-package-4.2.6.1-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 -Xms63g -XX:+UseParallelGC -XX:ParallelGCThreads=3 -jar /gatk/gatk-package-4.2.6.1-local.jar VariantRecalibrator -V gs://daly_schema2_gnomad_subset_vds/rye-test/outputs/subset_50_2000-vqsr-ready.vcf.bgz -O /io/batch/54f332/VQSR__SNPsVariantRecalibratorScattered-CkEY1/recalibration --tranches-file /io/batch/54f332/VQSR__SNPsVariantRecalibratorScattered-CkEY1/tranches --trust-all-polymorphic -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.8 -tranche 99.6 -tranche 99.5 -tranche 99.4 -tranche 99.3 -tranche 99.0 -tranche 98.0 -tranche 97.0 -tranche 90.0 -an AS_QD -an AS_MQRankSum -an AS_ReadPosRankSum -an AS_FS -an AS_MQ -mode SNP --max-gaussians 6 -resource:hapmap,known=false,training=true,truth=true,prior=15 gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz -resource:omni,known=false,training=true,truth=true,prior=12 gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz -resource:1000G,known=false,training=true,truth=false,prior=10 gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz -resource:dbsnp,known=true,training=false,truth=false,prior=7 gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.gz --use-allele-specific-annotations

Lindo Nkambule