GenomicsDBImport - why "intervals" is required??
AnsweredREQUIRED for all errors and issues:
a) GATK version used: gatk-4.2.4.0
b) Exact command used: gatk GenomicsDBImport -R /ddn/gs1/home/li11/project2017/exomeSeq/SangerWG/GRCm38_68_ref/GRCm38_68.fa --genomicsdb-workspace-path /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/testDir/PONtest/pon_db -V /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/NormalSamples/MD6831b_output_raw_snps_indels.vcf.gz -V /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/NormalSamples/MD6837b_output_raw_snps_indels.vcf.gz
c) Entire program log:
20:31:59.033 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/ddn/gs1/home/li11/tools/GATK/gatk-4.2.4.0/gatk-package-4.2.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
May 24, 2022 8:31:59 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
20:31:59.271 INFO GenomicsDBImport - ------------------------------------------------------------
20:31:59.272 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.4.0
20:31:59.272 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
20:31:59.272 INFO GenomicsDBImport - Executing as li11@ehshpclp134 on Linux v3.10.0-1127.19.1.el7.x86_64 amd64
20:31:59.272 INFO GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_92-b14
20:31:59.272 INFO GenomicsDBImport - Start Date/Time: May 24, 2022 8:31:58 PM EDT
20:31:59.272 INFO GenomicsDBImport - ------------------------------------------------------------
20:31:59.273 INFO GenomicsDBImport - ------------------------------------------------------------
20:31:59.273 INFO GenomicsDBImport - HTSJDK Version: 2.24.1
20:31:59.273 INFO GenomicsDBImport - Picard Version: 2.25.4
20:31:59.273 INFO GenomicsDBImport - Built for Spark Version: 2.4.5
20:31:59.274 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:31:59.274 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:31:59.274 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:31:59.274 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:31:59.274 INFO GenomicsDBImport - Deflater: IntelDeflater
20:31:59.274 INFO GenomicsDBImport - Inflater: IntelInflater
20:31:59.274 INFO GenomicsDBImport - GCS max retries/reopens: 20
20:31:59.274 INFO GenomicsDBImport - Requester pays: disabled
20:31:59.275 INFO GenomicsDBImport - Initializing engine
20:31:59.606 INFO GenomicsDBImport - Shutting down engine
[May 24, 2022 8:31:59 PM EDT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2207776768
***********************************************************************
A USER ERROR has occurred: No intervals specified
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /ddn/gs1/home/li11/tools/GATK/gatk-4.2.4.0/gatk-package-4.2.4.0-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 -jar /ddn/gs1/home/li11/tools/GATK/gatk-4.2.4.0/gatk-package-4.2.4.0-local.jar GenomicsDBImport -R /ddn
/gs1/home/li11/project2017/exomeSeq/SangerWG/GRCm38_68_ref/GRCm38_68.fa --genomicsdb-workspace-path /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/testDir/PONtest/pon_db -V /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/NormalSamples/MD6831b_out
put_raw_snps_indels.vcf.gz -V /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/NormalSamples/MD6837b_output_raw_snps_indels.vcf.gz
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Thank you for your post, Jianying Li! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.
Please see our Support Policy for more details about how we prioritize responding to questions.
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Thanks Genevieve! Here is the follow up question, in the help document the "intervel -L" is not required. But, when I issued for following command:gatk GenomicsDBImport -R /ddn/gs1/home/li11/project2017/exomeSeq/SangerWG/GRCm38_68_ref/GRCm38_68.fa --genomicsdb-workspace-path /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/testDir/PONtest/pon_db -V
/ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/NormalSamples/MD6831b_output_raw_snps_indels.vcf.gz -V /ddn/gs1/home/li11/project2022/ArunSummerSIP/NewSangleWGS/NormalSamples/MD6837b_output_raw_snps_indels
.vcf.gzIt complains with the log like:
A USER ERROR has occurred: No intervals specified
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Hi Jianying Li,
Please see the tool documentation for the detailed description of GenomicsDBImport. Intervals are required when creating a new GenomicsDB workspace:
At least one interval must be provided, unless incrementally importing new samples in which case specified intervals are ignored in favor of intervals specified in the existing workspace.
Let me know if you have any other questions.
Best,
Genevieve
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