VariantFiltration
Answered
Dear Sir/Madam
I have an error message in my Variant filtration step that stops without running. The error message differs with GATK4 version ( either 4.1.2.0 or 4.1.9.0). The 4.1.9.0 error message indicates an issue with "undefined variable" for MQRanqSum and ReadPosRankSum even though these parameters are defined in the vcf header and I could recover their profile using bcftools. With 4.1.2.0 the error message made a mention to the log4j:and .jexl2.JexlEngine, and in both cases, it ended up with
INFO VariantFiltration - Shutting down engine. The list of subsequent java description was identical with the two versions. Here I did use 4.1.9.0 for the joint genotyping step. In the past, I used 4.1.2.0 for joint genotyping and 4.1.2.0 for variant filtration with a very similar command on the same computer and it worked fine.
I provide here the two logs obtained with the two versions.
I thank you for your help and insights.
Best regards
Thierry
Using GATK jar /home/grange/miniconda2/envs/paleogenomic_python2_2019/share/gatk4-4.1.2.0-1/gatk-package-4.1.2.0-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/grange/miniconda2/envs/paleogenomic_python2_2019/share/gatk4-4.1.2.0-1/gatk-package-4.1.2.0-local.jar VariantFiltration -R /home/grange/Genomes/Bos/ARS_UCD1.2.Y/ARS-UCD1.2_Btau5.0.1Y.fa -V Cattle_December2020_2.vcf.gz -O Cattle_December2020_2_filter1.vcf.gz -filter QD < 2.0 --filter-name QD2 -filter SOR > 3.0 --filter-name SOR3 -filter FS > 60.0 --filter-name FS60 -filter MQRankSum < -10.0 --filter-name MQRankSum-10 -filter ReadPosRankSum < -3.0 --filter-name ReadPosRankSum-3 -filter MQRankSum > 10.0 --filter-name MQRankSum10 -filter ReadPosRankSum > 3 --filter-name ReadPosRankSum3
10:56:03.237 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/grange/miniconda2/envs/paleogenomic_python2_2019/share/gatk4-4.1.2.0-1/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Feb 25, 2021 10:56:04 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:56:04.994 INFO VariantFiltration - ------------------------------------------------------------
10:56:04.995 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.1.2.0
10:56:04.995 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/
10:56:04.995 INFO VariantFiltration - Executing as grange@neptune.ijm.univ-paris-diderot.priv on Linux v3.10.0-1062.4.3.el7.x86_64 amd64
10:56:04.995 INFO VariantFiltration - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01
10:56:04.996 INFO VariantFiltration - Start Date/Time: 25 février 2021 10:56:03 CET
10:56:04.996 INFO VariantFiltration - ------------------------------------------------------------
10:56:04.996 INFO VariantFiltration - ------------------------------------------------------------
10:56:04.997 INFO VariantFiltration - HTSJDK Version: 2.19.0
10:56:04.997 INFO VariantFiltration - Picard Version: 2.19.0
10:56:04.997 INFO VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:56:04.997 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:56:04.997 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:56:04.997 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:56:04.997 INFO VariantFiltration - Deflater: IntelDeflater
10:56:04.997 INFO VariantFiltration - Inflater: IntelInflater
10:56:04.998 INFO VariantFiltration - GCS max retries/reopens: 20
10:56:04.998 INFO VariantFiltration - Requester pays: disabled
10:56:04.998 INFO VariantFiltration - Initializing engine
10:56:05.372 INFO FeatureManager - Using codec VCFCodec to read file file:///run/media/grange/36To_Raid5/Cattle/SNP_calling/Cattle_December2020_2.vcf.gz
10:56:05.608 INFO VariantFiltration - Done initializing engine
10:56:05.697 INFO ProgressMeter - Starting traversal
10:56:05.697 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
log4j:WARN No appenders could be found for logger (org.apache.commons.jexl2.JexlEngine).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
10:56:05.726 INFO VariantFiltration - Shutting down engine
[25 février 2021 10:56:05 CET] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1884815360
java.lang.NumberFormatException: For input string: "0.00"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Long.parseLong(Long.java:589)
at java.lang.Long.parseLong(Long.java:631)
at org.apache.commons.jexl2.JexlArithmetic.toLong(JexlArithmetic.java:906)
at org.apache.commons.jexl2.JexlArithmetic.compare(JexlArithmetic.java:718)
at org.apache.commons.jexl2.JexlArithmetic.greaterThan(JexlArithmetic.java:790)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:796)
at org.apache.commons.jexl2.parser.ASTGTNode.jjtAccept(ASTGTNode.java:18)
at org.apache.commons.jexl2.Interpreter.interpret(Interpreter.java:232)
at org.apache.commons.jexl2.ExpressionImpl.evaluate(ExpressionImpl.java:65)
at htsjdk.variant.variantcontext.JEXLMap.evaluateExpression(JEXLMap.java:186)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:95)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:15)
at htsjdk.variant.variantcontext.VariantContextUtils.match(VariantContextUtils.java:338)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.matchesFilter(VariantFiltration.java:421)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.filter(VariantFiltration.java:380)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.apply(VariantFiltration.java:340)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:106)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:104)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Using GATK jar /home/grange/miniconda2/envs/gatk4-1-9/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-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/grange/miniconda2/envs/gatk4-1-9/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-local.jar VariantFiltration -R /home/grange/Genomes/Bos/ARS_UCD1.2.Y/ARS-UCD1.2_Btau5.0.1Y.fa -V Cattle_December2020_2.vcf.gz -O Cattle_December2020_2_filter1.vcf.gz -filter QD < 2.0 --filter-name QD2 -filter SOR > 3.0 --filter-name SOR3 -filter FS > 60.0 --filter-name FS60 -filter MQRankSum < -10.0 --filter-name MQRankSum-10 -filter ReadPosRankSum < -3.0 --filter-name ReadPosRankSum-3 -filter MQRankSum > 10.0 --filter-name MQRankSum10 -filter ReadPosRankSum > 3 --filter-name ReadPosRankSum3
11:02:10.553 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/grange/miniconda2/envs/gatk4-1-9/share/gatk4-4.1.9.0-0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Feb 25, 2021 11:02:10 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
11:02:10.716 INFO VariantFiltration - ------------------------------------------------------------
11:02:10.717 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.1.9.0
11:02:10.717 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/
11:02:10.717 INFO VariantFiltration - Executing as grange@neptune.ijm.univ-paris-diderot.priv on Linux v3.10.0-1062.4.3.el7.x86_64 amd64
11:02:10.717 INFO VariantFiltration - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_265-b11
11:02:10.717 INFO VariantFiltration - Start Date/Time: 25 février 2021 11:02:10 CET
11:02:10.717 INFO VariantFiltration - ------------------------------------------------------------
11:02:10.717 INFO VariantFiltration - ------------------------------------------------------------
11:02:10.718 INFO VariantFiltration - HTSJDK Version: 2.23.0
11:02:10.718 INFO VariantFiltration - Picard Version: 2.23.3
11:02:10.718 INFO VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:02:10.718 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:02:10.718 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:02:10.718 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:02:10.718 INFO VariantFiltration - Deflater: IntelDeflater
11:02:10.718 INFO VariantFiltration - Inflater: IntelInflater
11:02:10.718 INFO VariantFiltration - GCS max retries/reopens: 20
11:02:10.718 INFO VariantFiltration - Requester pays: disabled
11:02:10.718 INFO VariantFiltration - Initializing engine
11:02:11.335 INFO FeatureManager - Using codec VCFCodec to read file file:///run/media/grange/36To_Raid5/Cattle/SNP_calling/Cattle_December2020_2.vcf.gz
11:02:11.737 INFO VariantFiltration - Done initializing engine
11:02:11.839 INFO ProgressMeter - Starting traversal
11:02:11.839 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
11:02:11.861 WARN JexlEngine - ![0,9]: 'MQRankSum < -10.0;' undefined variable MQRankSum
11:02:11.862 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -3.0;' undefined variable ReadPosRankSum
11:02:11.862 WARN JexlEngine - ![0,9]: 'MQRankSum > 10.0;' undefined variable MQRankSum
11:02:11.862 WARN JexlEngine - ![0,14]: 'ReadPosRankSum > 3;' undefined variable ReadPosRankSum
11:02:11.868 WARN JexlEngine - ![0,9]: 'MQRankSum < -10.0;' undefined variable MQRankSum
11:02:11.868 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -3.0;' undefined variable ReadPosRankSum
11:02:11.868 WARN JexlEngine - ![0,9]: 'MQRankSum > 10.0;' undefined variable MQRankSum
11:02:11.868 WARN JexlEngine - ![0,14]: 'ReadPosRankSum > 3;' undefined variable ReadPosRankSum
11:02:11.869 WARN JexlEngine - ![0,9]: 'MQRankSum < -10.0;' undefined variable MQRankSum
11:02:11.869 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -3.0;' undefined variable ReadPosRankSum
11:02:11.870 WARN JexlEngine - ![0,9]: 'MQRankSum > 10.0;' undefined variable MQRankSum
11:02:11.870 WARN JexlEngine - ![0,14]: 'ReadPosRankSum > 3;' undefined variable ReadPosRankSum
11:02:11.875 INFO VariantFiltration - Shutting down engine
[25 février 2021 11:02:11 CET] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2113404928
java.lang.NumberFormatException: For input string: "0.00"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Long.parseLong(Long.java:589)
at java.lang.Long.parseLong(Long.java:631)
at org.apache.commons.jexl2.JexlArithmetic.toLong(JexlArithmetic.java:906)
at org.apache.commons.jexl2.JexlArithmetic.compare(JexlArithmetic.java:718)
at org.apache.commons.jexl2.JexlArithmetic.greaterThan(JexlArithmetic.java:790)
at org.apache.commons.jexl2.Interpreter.visit(Interpreter.java:796)
at org.apache.commons.jexl2.parser.ASTGTNode.jjtAccept(ASTGTNode.java:18)
at org.apache.commons.jexl2.Interpreter.interpret(Interpreter.java:232)
at org.apache.commons.jexl2.ExpressionImpl.evaluate(ExpressionImpl.java:65)
at htsjdk.variant.variantcontext.JEXLMap.evaluateExpression(JEXLMap.java:186)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:95)
at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:15)
at htsjdk.variant.variantcontext.VariantContextUtils.match(VariantContextUtils.java:338)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.matchesFilter(VariantFiltration.java:453)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.filter(VariantFiltration.java:407)
at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.apply(VariantFiltration.java:354)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
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)
-
Hi ThierryGrange,
The error message that exits the command for both GATK versions is the same:
java.lang.NumberFormatException: For input string: "0.00"
It is most likely occurring from an issue with your command. The MQRankSum10 filter has -filter ReadPosRankSum > 3. The 3 is being read as a string. If you change it to 3.0, it should fix this error message.
Here is more information about JEXL expressions in GATK: https://gatk.broadinstitute.org/hc/en-us/articles/360035891011-JEXL-filtering-expressions
There have been a few changes in VariantFiltration since GATK 4.1.2.0, which might be why you are seeing a different stack trace message. See if the fix I mentioned above helps the command run, and then let me know if you would like more information as well regarding the warnings.
Best,
Genevieve
-
Thanks for noticing the problem. It started.properly using GATK 4.1.2.0. With 4.1.9.0, it seems to proceed but it writes in the log
WARN JexlEngine - ![0,9]: 'MQRankSum > 10.0;' undefined variable MQRankSum
WARN JexlEngine - ![0,14]: 'ReadPosRankSum > 3.0;' undefined variable ReadPosRankSumat every position. I am not sure it will proceed properly to the end given this error message so I preferred to use GATK 4.1.2.0 as the log is more as I am used to.
Thanks for your help.
Best
Thierry
-
Hi Thierry,
I would recommend using the more recent version of GATK because we have made some updates to VariantFiltration since 4.1.2.0.
The log warning messages are just warnings, indicating that the annotation does not exist at those sites. Sometimes annotations cannot be calculated at certain sites, it does not mean there is an issue.
The MQRankSum and ReadPosRankSum are not calculated at sites where there are no heterozygous individuals. The mix of ref and alt reads are needed to calculate these values. This is most likely why you see this warning at some of your sites. It would be fine to proceed with these warnings because you also have other filters in your command.
I found this information at our legacy forum site, but rewrote it here for other users who get these warnings in the future. See this link to find the original text at the legacy forum site: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/2017-01-18-2016-08-11/8323-Why-do-MQRankSum-and-ReadPosRankSum-not-appear-in-some-vcf-file-entries
Best,
Genevieve
-
Hi Genevieve,
I also get such warnings for QD filter but only for few iterations (log provided below). I trust this is okay but still your confirmation will help.
Kind regards,
Sanjeev
12:45:31.689 INFO IntervalArgumentCollection - Processing 88663952 bp from intervals
12:45:31.694 INFO VariantFiltration - Done initializing engine
12:45:31.794 INFO ProgressMeter - Starting traversal
12:45:31.795 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
12:45:35.801 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:45:41.876 INFO ProgressMeter - ST4.03ch01:1606030 0.2 31000 184523.8
12:45:52.049 INFO ProgressMeter - ST4.03ch01:3113185 0.3 66000 195526.6
12:46:02.257 INFO ProgressMeter - ST4.03ch01:4919474 0.5 103000 202875.7
12:46:12.265 INFO ProgressMeter - ST4.03ch01:7510765 0.7 141000 209048.9
12:46:22.374 INFO ProgressMeter - ST4.03ch01:11128057 0.8 183000 217090.4
12:46:32.420 INFO ProgressMeter - ST4.03ch01:14472881 1.0 223000 220701.0
12:46:42.553 INFO ProgressMeter - ST4.03ch01:17237870 1.2 268000 227253.5
12:46:45.314 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:46:52.630 INFO ProgressMeter - ST4.03ch01:20794730 1.3 313000 232325.1
12:47:02.700 INFO ProgressMeter - ST4.03ch01:23409726 1.5 357000 235630.6
12:47:12.868 INFO ProgressMeter - ST4.03ch01:27205716 1.7 401000 238045.8
12:47:17.241 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:47:22.965 INFO ProgressMeter - ST4.03ch01:30944830 1.9 445000 240172.7
12:47:33.016 INFO ProgressMeter - ST4.03ch01:33150597 2.0 488000 241542.3
12:47:43.201 INFO ProgressMeter - ST4.03ch01:35710172 2.2 532000 242911.3
12:47:53.319 INFO ProgressMeter - ST4.03ch01:37751639 2.4 575000 243774.9
12:48:03.416 INFO ProgressMeter - ST4.03ch01:40991337 2.5 621000 245745.9
12:48:13.487 INFO ProgressMeter - ST4.03ch01:44373341 2.7 664000 246394.4
12:48:23.692 INFO ProgressMeter - ST4.03ch01:46978725 2.9 707000 246775.7
12:48:33.868 INFO ProgressMeter - ST4.03ch01:49758934 3.0 752000 247814.1
12:48:43.915 INFO ProgressMeter - ST4.03ch01:53352745 3.2 796000 248594.6
12:48:54.101 INFO ProgressMeter - ST4.03ch01:55476603 3.4 839000 248832.2
12:49:04.138 INFO ProgressMeter - ST4.03ch01:58080475 3.5 882000 249219.4
12:49:14.222 INFO ProgressMeter - ST4.03ch01:60423711 3.7 923000 248981.7
12:49:24.456 INFO ProgressMeter - ST4.03ch01:62452241 3.9 963000 248344.2
12:49:31.313 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:49:34.577 INFO ProgressMeter - ST4.03ch01:64472664 4.0 1002000 247629.6
12:49:44.607 INFO ProgressMeter - ST4.03ch01:66229834 4.2 1040000 246823.7
12:49:54.717 INFO ProgressMeter - ST4.03ch01:68087542 4.4 1078000 246004.5
12:50:03.323 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:50:04.911 INFO ProgressMeter - ST4.03ch01:70284047 4.6 1117000 245390.2
12:50:15.109 INFO ProgressMeter - ST4.03ch01:72134705 4.7 1155000 244604.9
12:50:15.256 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:50:16.325 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:50:25.111 INFO ProgressMeter - ST4.03ch01:73737193 4.9 1192000 243832.6
12:50:35.355 INFO ProgressMeter - ST4.03ch01:75379330 5.1 1230000 243115.0
12:50:45.480 INFO ProgressMeter - ST4.03ch01:77011718 5.2 1267000 242345.0
12:50:55.511 INFO ProgressMeter - ST4.03ch01:78473744 5.4 1304000 241693.3
12:50:58.613 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:51:05.583 INFO ProgressMeter - ST4.03ch01:79954532 5.6 1341000 241051.2
12:51:15.606 INFO ProgressMeter - ST4.03ch01:81396719 5.7 1378000 240481.0
12:51:25.853 INFO ProgressMeter - ST4.03ch01:82841016 5.9 1416000 239960.7
12:51:35.870 INFO ProgressMeter - ST4.03ch01:84271130 6.1 1453000 239456.2
12:51:44.919 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:51:45.890 INFO ProgressMeter - ST4.03ch01:85589325 6.2 1490000 238976.7
12:51:55.899 INFO ProgressMeter - ST4.03ch01:87145632 6.4 1527000 238529.1
12:51:56.739 WARN JexlEngine - ![0,2]: 'QD < 2.0;' undefined variable QD
12:52:05.261 INFO ProgressMeter - ST4.03ch01:88587959 6.6 1561835 238165.7
12:52:05.262 INFO ProgressMeter - Traversal complete. Processed 1561835 total variants in 6.6 minutes.
12:52:05.278 INFO VariantFiltration - Shutting down engine
[10 July 2021 12:52:05 BST] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 6.59 minutes.
Runtime.totalMemory()=778567680 -
Hi sanjeevksh,
Each annotation is different so for your case you'll want to look at the QualByDepth documentation to make sure it might not occur at all locations: https://gatk.broadinstitute.org/hc/en-us/articles/360056968272-QualByDepth
This annotation only is applied at sites where there is a variant allele genotyped. So, if you have a file containing some sites where there is the reference allele, then that would explain your warnings. You can double check that the QD annotation occurs where you expect by inspecting some variant sites and making sure that they have the QD annotation.
Hope this helps!
Genevieve
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Hi Genevieve,
Thank you for your feedback, this is very helpful!
Kind regards,
Sanjeev
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No problem!
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