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WGLab / SeqMule

Automated human exome/genome variants detection from FASTQ files
http://seqmule.usc.edu
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java.lang.IllegalArgumentException:#gatk#variantcalling #174

Open ashaneev opened 5 years ago

ashaneev commented 5 years ago

I've tried with the following command for variant calling through gatk. But it didn't create any out file.

./gatk VariantFiltration -R /home/Documents/Tools_NGS/VariantCall/genome_assembly.fa -V /media/TOSHIBAEXT/Variant_Calling/variantData/snps_300bp.vcf.gz -O snp_output.vcf.gz --filter-expression "AB < 0.2 || MQ0 > 50"

Using GATK jar /home/Documents/Tools_NGS/gatk-4.0.6.0/gatk-package-4.0.6.0-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 /home/Documents/Tools_NGS/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar VariantFiltration -R /home/Documents/Tools_NGS/VariantCall/genome_assembly.fa -V /media/TOSHIBAEXT/Variant_Calling/variantData/snps_300bp.vcf.gz -O snp_output.vcf.gz --filter-expression AB < 0.2 || MQ0 > 50 12:29:04.413 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/Documents/Tools_NGS/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:29:08.256 INFO VariantFiltration - ------------------------------------------------------------ 12:29:08.257 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.0.6.0 12:29:08.257 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:29:08.257 INFO VariantFiltration - Executing as home@home-Lenovo-H30-50 on Linux v4.4.0-31-generic amd64 12:29:08.257 INFO VariantFiltration - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_171-b11 12:29:08.257 INFO VariantFiltration - Start Date/Time: 26 September, 2018 12:29:04 PM IST 12:29:08.257 INFO VariantFiltration - ------------------------------------------------------------ 12:29:08.257 INFO VariantFiltration - ------------------------------------------------------------ 12:29:08.258 INFO VariantFiltration - HTSJDK Version: 2.16.0 12:29:08.258 INFO VariantFiltration - Picard Version: 2.18.7 12:29:08.258 INFO VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:29:08.258 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:29:08.258 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:29:08.258 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:29:08.258 INFO VariantFiltration - Deflater: IntelDeflater 12:29:08.258 INFO VariantFiltration - Inflater: IntelInflater 12:29:08.258 INFO VariantFiltration - GCS max retries/reopens: 20 12:29:08.258 INFO VariantFiltration - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 12:29:08.258 INFO VariantFiltration - Initializing engine 12:29:10.301 INFO FeatureManager - Using codec VCFCodec to read file file:///media/TOSHIBAEXT/Variant_Calling/variantData/snps_300bp.vcf.gz 12:29:11.469 INFO VariantFiltration - Done initializing engine 12:29:11.471 INFO VariantFiltration - Shutting down engine [26 September, 2018 12:29:11 PM IST] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=576192512 java.lang.IllegalArgumentException: Inconsistent number of provided filter names and expressions: names=[] exps=[AB < 0.2 || MQ0 > 50] at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:238) at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:259) at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.onTraversalStart(VariantFiltration.java:284) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:982) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199) 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)

Please help me to find a solution for this..thankyou.

yunfeiguo commented 5 years ago

gatk complained

java.lang.IllegalArgumentException: Inconsistent number of provided filter names and expressions: names=[] exps=[AB < 0.2 || MQ0 > 50]

please refer to https://gatkforums.broadinstitute.org/gatk/discussion/4737/error-during-filtering-variant-step

Thanks.

On Wed, Sep 26, 2018 at 3:37 AM ashaneev notifications@github.com wrote:

I've tried with the following command for variant calling through gatk. But it didn't create any out file.

./gatk VariantFiltration -R /home/Documents/Tools_NGS/VariantCall/genome_assembly.fa -V /media/TOSHIBAEXT/Variant_Calling/variantData/snps_300bp.vcf.gz -O snp_output.vcf.gz --filter-expression "AB < 0.2 || MQ0 > 50"

Using GATK jar /home/Documents/Tools_NGS/gatk-4.0.6.0/gatk-package-4.0.6.0-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 /home/Documents/Tools_NGS/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar VariantFiltration -R /home/Documents/Tools_NGS/VariantCall/genome_assembly.fa -V /media/TOSHIBAEXT/Variant_Calling/variantData/snps_300bp.vcf.gz -O snp_output.vcf.gz --filter-expression AB < 0.2 || MQ0 > 50 12:29:04.413 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/Documents/Tools_NGS/gatk-4.0.6.0/gatk-package-4.0.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:29:08.256 INFO VariantFiltration -

12:29:08.257 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.0.6.0 12:29:08.257 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:29:08.257 INFO VariantFiltration - Executing as home@home-Lenovo-H30-50 on Linux v4.4.0-31-generic amd64 12:29:08.257 INFO VariantFiltration - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_171-b11 12:29:08.257 INFO VariantFiltration - Start Date/Time: 26 September, 2018 12:29:04 PM IST 12:29:08.257 INFO VariantFiltration -

12:29:08.257 INFO VariantFiltration -

12:29:08.258 INFO VariantFiltration - HTSJDK Version: 2.16.0 12:29:08.258 INFO VariantFiltration - Picard Version: 2.18.7 12:29:08.258 INFO VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:29:08.258 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:29:08.258 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:29:08.258 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:29:08.258 INFO VariantFiltration - Deflater: IntelDeflater 12:29:08.258 INFO VariantFiltration - Inflater: IntelInflater 12:29:08.258 INFO VariantFiltration - GCS max retries/reopens: 20 12:29:08.258 INFO VariantFiltration - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes 12:29:08.258 INFO VariantFiltration - Initializing engine 12:29:10.301 INFO FeatureManager - Using codec VCFCodec to read file file:///media/TOSHIBAEXT/Variant_Calling/variantData/snps_300bp.vcf.gz 12:29:11.469 INFO VariantFiltration - Done initializing engine 12:29:11.471 INFO VariantFiltration - Shutting down engine [26 September, 2018 12:29:11 PM IST] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=576192512 java.lang.IllegalArgumentException: Inconsistent number of provided filter names and expressions: names=[] exps=[AB < 0.2 || MQ0 > 50] at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:238) at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:259) at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.onTraversalStart(VariantFiltration.java:284) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:982) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199) 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)

Please help me to find a solution for this..thankyou.

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