Error while running HaplotypeCaller
REQUIRED for all errors and issues:
a) GATK version used: v4.3.0.0
b) Exact command used: gatk --java-options "-Xmx8g" HaplotypeCaller -R Data/index/Gmax.a4.v1.fasta -I Data/Outputs/output_wgs.bam -O raw_variants.vcf
c) Entire program log: Using GATK jar /home/achint/anaconda3/envs/myenv/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-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 -Xmx4g -jar /home/achint/anaconda3/envs/myenv/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar HaplotypeCaller -R Data/index/Gmax.a4.v1.fasta -I Data/Outputs/output_wgs.bam -O raw_variants.vcf
19:19:28.895 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/achint/anaconda3/envs/myenv/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
19:19:28.990 INFO HaplotypeCaller - ------------------------------------------------------------
19:19:28.990 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.3.0.0
19:19:28.990 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
19:19:28.990 INFO HaplotypeCaller - Executing as achint@achint-OptiPlex-5060 on Linux v5.19.0-32-generic amd64
19:19:28.990 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_332-b09
19:19:28.990 INFO HaplotypeCaller - Start Date/Time: 19 February, 2023 7:19:28 PM IST
19:19:28.990 INFO HaplotypeCaller - ------------------------------------------------------------
19:19:28.990 INFO HaplotypeCaller - ------------------------------------------------------------
19:19:28.991 INFO HaplotypeCaller - HTSJDK Version: 3.0.1
19:19:28.991 INFO HaplotypeCaller - Picard Version: 2.27.5
19:19:28.991 INFO HaplotypeCaller - Built for Spark Version: 2.4.5
19:19:28.991 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:19:28.991 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:19:28.991 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:19:28.991 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:19:28.991 INFO HaplotypeCaller - Deflater: IntelDeflater
19:19:28.991 INFO HaplotypeCaller - Inflater: IntelInflater
19:19:28.991 INFO HaplotypeCaller - GCS max retries/reopens: 20
19:19:28.991 INFO HaplotypeCaller - Requester pays: disabled
19:19:28.991 INFO HaplotypeCaller - Initializing engine
19:19:29.242 INFO HaplotypeCaller - Done initializing engine
19:19:29.258 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
19:19:29.260 INFO HaplotypeCaller - Shutting down engine
[19 February, 2023 7:19:29 PM IST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=417857536
java.lang.IllegalStateException: the sample list cannot be null or empty
at org.broadinstitute.hellbender.utils.Utils.validate(Utils.java:814)
at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.<init>(GenotypingEngine.java:69)
at org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine.<init>(MinimalGenotypingEngine.java:46)
at org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine.<init>(MinimalGenotypingEngine.java:35)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initializeActiveRegionEvaluationGenotyperEngine(HaplotypeCallerEngine.java:373)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initialize(HaplotypeCallerEngine.java:239)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.<init>(HaplotypeCallerEngine.java:196)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.buildHaplotypeCallerEngine(HaplotypeCaller.java:262)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.onTraversalStart(HaplotypeCaller.java:253)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1093)
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)
-
Hello Achint Kumar, Can you check that you have a valid bam header for Data/Outputs/output_wgs.bam? That error could be generated if there is an issue extracting the SM tag from the RG IDs for from the bam header. I would like to diagnose what is causing this stack-trace since you shouldn't be seeing that at all. You can run `$ samtools view -H __.bam` to view the header and you should see a bunch of @rg fields with the SM:<SAMPLENAME>. How was your bam generated and can you make sure that its generating a valid bam header?
Please sign in to leave a comment.
1 comment