Instructions

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Bug Report

03:51:59.035 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jul 13, 2023 3:51:59 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
03:51:59.220 INFO GenotypeGVCFs - ------------------------------------------------------------
03:51:59.220 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.2.0.0
03:51:59.220 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
03:51:59.220 INFO GenotypeGVCFs - Executing as dingrj@localhost.localdomain on Linux v4.18.0-348.7.1.el8_5.x86_64 amd64
03:51:59.220 INFO GenotypeGVCFs - Java runtime: OpenJDK 64-Bit Server VM v11.0.11+9-Ubuntu-0ubuntu2.18.04
03:51:59.220 INFO GenotypeGVCFs - Start Date/Time: July 13, 2023 at 3:51:58 AM UTC
03:51:59.221 INFO GenotypeGVCFs - ------------------------------------------------------------
03:51:59.221 INFO GenotypeGVCFs - ------------------------------------------------------------
03:51:59.221 INFO GenotypeGVCFs - HTSJDK Version: 2.24.0
03:51:59.221 INFO GenotypeGVCFs - Picard Version: 2.25.0
03:51:59.221 INFO GenotypeGVCFs - Built for Spark Version: 2.4.5
03:51:59.221 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
03:51:59.221 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
03:51:59.221 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
03:51:59.221 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
03:51:59.221 INFO GenotypeGVCFs - Deflater: IntelDeflater
03:51:59.221 INFO GenotypeGVCFs - Inflater: IntelInflater
03:51:59.221 INFO GenotypeGVCFs - GCS max retries/reopens: 20
03:51:59.222 INFO GenotypeGVCFs - Requester pays: disabled
03:51:59.222 INFO GenotypeGVCFs - Initializing engine
03:51:59.571 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.3.2-e18fa63
11:51:59.957 info NativeGenomicsDB - pid=1480681 tid=1480682 No valid combination operation found for INFO field InbreedingCoeff - the field will NOT be part of INFO fields in the generated VCF records
11:51:59.957 info NativeGenomicsDB - pid=1480681 tid=1480682 No valid combination operation found for INFO field MLEAC - the field will NOT be part of INFO fields in the generated VCF records
11:51:59.957 info NativeGenomicsDB - pid=1480681 tid=1480682 No valid combination operation found for INFO field MLEAF - the field will NOT be part of INFO fields in the generated VCF records
03:52:00.341 INFO GenotypeGVCFs - Done initializing engine
03:52:00.369 INFO ProgressMeter - Starting traversal
03:52:00.369 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
03:52:00.377 INFO GenotypeGVCFs - Shutting down engine
[July 13, 2023 at 3:52:00 AM UTC] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2583691264
java.lang.IllegalStateException: There are no sources based on those query parameters
at org.genomicsdb.reader.GenomicsDBFeatureIterator.(GenomicsDBFeatureIterator.java:167)
at org.genomicsdb.reader.GenomicsDBFeatureReader.query(GenomicsDBFeatureReader.java:152)
at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:569)
at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:538)
at org.broadinstitute.hellbender.engine.FeatureDataSource.query(FeatureDataSource.java:504)
at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$2(VariantLocusWalker.java:149)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.base/java.util.stream.ReferencePipeline$Head.forEachOrdered(ReferencePipeline.java:668)
at org.broadinstitute.hellbender.engine.VariantLocusWalker.traverse(VariantLocusWalker.java:148)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1058)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
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)
Using GATK jar /opt/gatk-4.2.0.0/gatk-package-4.2.0.0-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 -Xmx56g -Djava.io.tmpdir=./tmp -jar /opt/gatk-4.2.0.0/gatk-package-4.2.0.0-local.jar GenotypeGVCFs -R ../../01.ref/MS/genome.fasta -V gendb://genomeDB.Chr23 -all-sites -O Chr23.raw.vcf.gz

Affected tool(s) or class(es)

Tool/class name(s), special parameters?

Affected version(s)

• Latest public release version [version?] V4.2.0.0
• Latest master branch as of [date of test?]

Description

Describe the problem below. Provide screenshots , stacktrace , logs where appropriate.
There are no results generated.

Steps to reproduce

Tell us how to reproduce this issue. If possible, include command lines that reproduce the problem. (The support team may follow up to ask you to upload data to reproduce the issue.)

1:singularity exec ~/biosoft/resequence/Reseq_genek.sif gatk --java-options "-Xmx48g -Djava.io.tmpdir=./tmp" HaplotypeCaller -R ../../01.ref/MS/genome.fasta -I ../../02.mapping/MS/F10.sort.markdup.bam -L Chr01 -ERC GVCF -O F10/F10.Chr01.g.vcf.gz
2:singularity exec ~/biosoft/resequence/Reseq_genek.sif gatk --java-options "-Xmx56g -Djava.io.tmpdir=./tmp -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" GenomicsDBImport --sample-name-map gvcf.Chr01.map --genomicsdb-workspace-path genomeDB.Chr01 -L Chr01 --reader-threads 56 --batch-size 50 --tmp-dir ./tmp
3：singularity exec ~/biosoft/resequence/Reseq_genek.sif gatk --java-options "-Xmx56g -Djava.io.tmpdir=./tmp" GenotypeGVCFs -R ../../01.ref/MS/genome.fasta -V gendb://genomeDB.Chr01 -all-sites -O Chr01.raw.vcf.gz

Expected behavior

Tell us what should happen

Actual behavior

Tell us what happens instead

Feature request

Tool(s) or class(es) involved

Tool/class name(s), special parameters?

Description

Specify whether you want a modification of an existing behavior or addition of a new capability.
Provide examples, screenshots, where appropriate.

Documentation request

Tool(s) or class(es) involved

Tool/class name(s), parameters?

Description

Describe what needs to be added or modified.