FilterMutectCalls Problems
Before FilterMutectCalls,every process is success,but FilterMutectCalls Returns an empty cf file and does not report an error
that's my code!
gatk FilterMutectCalls -R /mnt/data2/yl_work/wes/00_ref/human/GRCh38.p13.genome.fa -V /mnt/data2/yl_work/wes/mutect/SOC1135.mutect2.vcf --ob-priors read-orientation-model.tar.gz --intervals /mnt/data2/yl_work/wes/00_ref/S07604514_AllTracks.bed -O /mnt/data2/yl_work/wes/mutect/SOC1135.mutect2.filter.vcf
Using GATK jar /home/yl/.conda/envs/wgs/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-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 -jar /home/yl/.conda/envs/wgs/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R /mnt/data2/yl_work/wes/00_ref/human/GRCh38.p13.genome.fa -V /mnt/data2/yl_work/wes/mutect/SOC1135.mutect2.vcf --ob-priors read-orientation-model.tar.gz --intervals /mnt/data2/yl_work/wes/00_ref/S07604514_AllTracks.bed -O /mnt/data2/yl_work/wes/mutect/SOC1135.mutect2.filter.vcf
17:07:28.975 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/yl/.conda/envs/wgs/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
17:07:29.120 INFO FilterMutectCalls - ------------------------------------------------------------
17:07:29.124 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
17:07:29.124 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
17:07:29.124 INFO FilterMutectCalls - Executing as yl@6601 on Linux v6.8.0-45-generic amd64
17:07:29.125 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.3-internal+0-adhoc..src
17:07:29.125 INFO FilterMutectCalls - Start Date/Time: 2024年10月9日 CST 下午5:07:28
17:07:29.125 INFO FilterMutectCalls - ------------------------------------------------------------
17:07:29.125 INFO FilterMutectCalls - ------------------------------------------------------------
17:07:29.126 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
17:07:29.127 INFO FilterMutectCalls - Picard Version: 3.1.1
17:07:29.127 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
17:07:29.127 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:07:29.127 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:07:29.127 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:07:29.128 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:07:29.128 INFO FilterMutectCalls - Deflater: IntelDeflater
17:07:29.128 INFO FilterMutectCalls - Inflater: IntelInflater
17:07:29.128 INFO FilterMutectCalls - GCS max retries/reopens: 20
17:07:29.128 INFO FilterMutectCalls - Requester pays: disabled
17:07:29.129 INFO FilterMutectCalls - Initializing engine
17:07:29.337 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/data2/yl_work/wes/mutect/SOC1135.mutect2.vcf
17:07:29.407 INFO FeatureManager - Using codec BEDCodec to read file file:///mnt/data2/yl_work/wes/00_ref/S07604514_AllTracks.bed
17:07:32.110 INFO IntervalArgumentCollection - Processing 63880654 bp from intervals
17:07:32.173 INFO FilterMutectCalls - Done initializing engine
17:07:32.266 INFO IOUtils - Extracting data from archive: file:///mnt/data2/yl_work/wes/read-orientation-model.tar.gz
17:07:32.275 INFO IOUtils - Extracting file: ./SOC1135.orientation_priors
17:07:32.304 INFO ProgressMeter - Starting traversal
17:07:32.304 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
17:07:32.305 INFO FilterMutectCalls - Starting pass 0 through the variants
17:07:32.346 INFO FilterMutectCalls - Shutting down engine
[2024年10月9日 CST 下午5:07:32] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1224736768
java.util.NoSuchElementException: No value present
at java.base/java.util.Optional.get(Optional.java:143)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilteredHaplotypeFilter.calculateErrorProbability(FilteredHaplotypeFilter.java:35)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2VariantFilter.errorProbabilities(Mutect2VariantFilter.java:23)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities.lambda$new$0(ErrorProbabilities.java:27)
at java.base/java.util.stream.Collectors.lambda$toMap$68(Collectors.java:1674)
at java.base/java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1625)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities.<init>(ErrorProbabilities.java:25)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.accumulateData(Mutect2FilteringEngine.java:138)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.nthPassApply(FilterMutectCalls.java:154)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverse$0(MultiplePassVariantWalker.java:40)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverseVariants$1(MultiplePassVariantWalker.java:77)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverseVariants(MultiplePassVariantWalker.java:75)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:40)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
at org.broadinstitute.hellbender.Main.main(Main.java:306)
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Hi lei yang
Does Mutect2 produce a proper VCF output? Do you observe calls in that file?
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Thanks for your reply, I think Mutect2 produces a proper vcf . File size is 4M
##tumor_sample=S1135
#CHROM POS ID REF ALT QUAL FILTER INFO
chr1 14932 . G T . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=2;MBQ=40,33;MFRL=393,306;MMQ=22,22;MPOS=36;POPAF=2.00;TLOD=3.72
chr1 14937 . T C . . AS_SB_TABLE=0,0|0,0;DP=2;ECNT=2;MBQ=35,28;MFRL=393,306;MMQ=22,22;MPOS=31;POPAF=2.11;TLOD=3.72
chr1 19004 . A G . . AS_SB_TABLE=3,0|2,0;DP=5;ECNT=1;MBQ=33,28;MFRL=353,348;MMQ=22,21;MPOS=19;POPAF=0.357;TLOD=3.27
chr1 135465 . C T . . AS_SB_TABLE=0,2|0,2;DP=4;ECNT=1;MBQ=28,33;MFRL=379,325;MMQ=40,40;MPOS=19;POPAF=0.650;TLOD=6.08 -
Hi lei yang
Are these the whole variant contexts from the VCF? Are you using the parameter below?
--sites-only-vcf-output
These variant contexts do not have any genotype information therefore it is probably normal that FilterMutectCalls is not working.
Let us know what your Mutect2 parameters are and if you are performing any other post processing before FilterMutectCalls step.
Regards.
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