BQSR Illegal Argument Exceptions
REQUIRED for all errors and issues:
a) GATK version used: 4.2.6.1
b) Exact command used:
gatk BaseRecalibrator \
-I ~/sv/53bp1_data/53bp1ko_L3.MD.bam \
-R ~/hg38/hg38.fa \
--known-sites ~/sv/dbSNP/dbSnp155Common.bed \
-O ~/sv/53bp1_data/53bp1ko_recal_data.table
c) Entire program log:
Using GATK jar /opt/applications/gatk/4.2.6.1/gatk-package-4.2.6.1-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 /opt/applications/gatk/4.2.6.1/gatk-package-4.2.6.1-local.jar BaseRecalibrator -I /gpfs/home/asun/sv/53bp1_data/53bp1ko_L3.MD.bam -R /gpfs/home/asun/hg38/hg38.fa --known-sites /gpfs/home/asun/sv/dbSNP/dbSnp155Common.bed -O /gpfs/home/asun/sv/53bp1_data/53bp1ko_recal_data.table
15:47:35.981 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/applications/gatk/4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
15:47:41.466 INFO BaseRecalibrator - ------------------------------------------------------------
15:47:41.467 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.6.1
15:47:41.467 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:47:41.468 INFO BaseRecalibrator - Executing as asun@nodea1321.cluster.net on Linux v3.10.0-1160.76.1.el7.x86_64 amd64
15:47:41.468 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_392-b08
15:47:41.469 INFO BaseRecalibrator - Start Date/Time: January 4, 2024 3:47:35 PM PST
15:47:41.469 INFO BaseRecalibrator - ------------------------------------------------------------
15:47:41.469 INFO BaseRecalibrator - ------------------------------------------------------------
15:47:41.470 INFO BaseRecalibrator - HTSJDK Version: 2.24.1
15:47:41.470 INFO BaseRecalibrator - Picard Version: 2.27.1
15:47:41.470 INFO BaseRecalibrator - Built for Spark Version: 2.4.5
15:47:41.470 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:47:41.470 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:47:41.470 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:47:41.470 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:47:41.471 INFO BaseRecalibrator - Deflater: IntelDeflater
15:47:41.471 INFO BaseRecalibrator - Inflater: IntelInflater
15:47:41.471 INFO BaseRecalibrator - GCS max retries/reopens: 20
15:47:41.471 INFO BaseRecalibrator - Requester pays: disabled
15:47:41.471 INFO BaseRecalibrator - Initializing engine
15:47:42.225 INFO FeatureManager - Using codec BEDCodec to read file file:///gpfs/home/asun/sv/dbSNP/dbSnp155Common.bed
15:47:42.422 WARN IndexUtils - Feature file "file:///gpfs/home/asun/sv/dbSNP/dbSnp155Common.bed" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
15:47:42.527 INFO BaseRecalibrator - Done initializing engine
15:47:42.530 INFO BaseRecalibrationEngine - The covariates being used here:
15:47:42.531 INFO BaseRecalibrationEngine - ReadGroupCovariate
15:47:42.531 INFO BaseRecalibrationEngine - QualityScoreCovariate
15:47:42.531 INFO BaseRecalibrationEngine - ContextCovariate
15:47:42.531 INFO BaseRecalibrationEngine - CycleCovariate
15:47:42.548 INFO ProgressMeter - Starting traversal
15:47:42.549 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
15:47:44.499 INFO BaseRecalibrator - Shutting down engine
[January 4, 2024 3:47:44 PM PST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=2123366400
java.lang.IllegalArgumentException: fromIndex(136) > toIndex(135)
at java.util.Arrays.rangeCheck(Arrays.java:113)
at java.util.Arrays.fill(Arrays.java:3044)
at org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.calculateKnownSites(BaseRecalibrationEngine.java:355)
at org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.calculateSkipArray(BaseRecalibrationEngine.java:324)
at org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.processRead(BaseRecalibrationEngine.java:139)
at org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator.apply(BaseRecalibrator.java:189)
at org.broadinstitute.hellbender.engine.ReadWalker.lambda$traverse$0(ReadWalker.java:100)
at java.util.stream.ForEachOps$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.ReadWalker.traverse(ReadWalker.java:98)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
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,
I am trying to use GATK best practices pre-processing for variant discovery. I am using bwa mem to align my data with UCSC's hg38 data, and using dbSNP version 155 from UCSC as well. I have also made sure to add read groups to my bam files. I am not sure what is wrong with this?
I am also considering using GATK's resource package to realign my data, but I am unsure if that is the issue here?
Thank you.
-
Hi Alexander Sun,
This error could be caused by an unusual/problematic CIGAR string in one of your reads. For example, a CIGAR beginning/ending with a deletion. Have you tried running ValidateSamFile on your bam? Unfortunately the error message does not tell us the specific site where the failure occurred. If you're able to share your inputs to BQSR with us, we'd likely be able to track down the source of the error for you.
Regards,
David
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