Haplotype Caller (4.1.6.0) : java.lang.IllegalStateException: Smith-Waterman alignment failure.

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Yokofakun

• March 28, 2020 16:41
• Edited

Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.

 

following https://gatk.broadinstitute.org/hc/en-us/community/posts/360059684672-Custom-ReadFilter-to-ignore-malformed-reads-

I switched to 4.1.6.0 this morning. I use the same command linen, but I now have a new error:

<pre>

java.lang.IllegalStateException: Smith-Waterman alignment failure. Cigar = 275M with reference length 275 but expecting referenc
e length of 303 ref = GGACTGGTCATCAGCTACCCCGAGACCAGGACTGGTCATCAGCTACCCCGAGACCAGGACTGGTCATCAGCTACCCCGAGACCAGGACTGGTCATCAGCTACCCCG
AGACCAGGACTGGTCATCAGCTACCCCGAGAACAGGACTGGTCATCAGCTACCCCGAGACCAGGACTGGTCATCAGCTACCCCGAGACCAGGACTGGTCATCAGCTACCCCGAGACCAGGACTGGTCA
TCAGCTACTCCGAGACCAGCATGGAGAGGTTTGCTGATGGTTGGCTGACTGCTAGTGTGAGCACTTGTC path GGACTGGTCATCAGCTACCCCGAGACCAGGACTGGTCATCAGCTACCCCGAGA
CCAGGACTGGTCATCAGCTACCCCGAGACCAGGACTGGTCATCAGCTACCCCGAGAACAGGACTGGTCATCAGCTACCCCGAGAACAGGACTGGTCATCAGCTACCCCGAGACCAGGACTGGTCATCA
GCTACCCCGAGACCAGGACTGGTCATCAGCTACTCCGAGACCAGCATGGAGAGGTTTGCTGATGGTTGGCTGACTGCTAGTGTGAGCACTTGTC
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.findBestPaths(ReadTh
readingAssembler.java:354)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.assembleKmerGraphsAn
dHaplotypeCall(ReadThreadingAssembler.java:196)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler.runLocalAssembly(Rea
dThreadingAssembler.java:146)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils.assembleReads(AssemblyBasedCalle
rUtils.java:269)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.ja
va:541)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:212)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
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:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)

</pre>

can you please help me,

 

thanks

 

P.

 

0

• 

  Yokofakun

  • March 29, 2020 10:48

  Furthemore, I uploaded a minimal BAM with the error in the corresponding github issue: https://github.com/broadinstitute/gatk/issues/6490#issuecomment-605617217

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• 

  Bhanu Gandham

  • March 30, 2020 22:40

  Hi Yokofakun

   

  Looks like a bug report has been opened for this issue. You can follow its progress here: https://github.com/broadinstitute/gatk/issues/6529

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  Bhanu Gandham

  • April 01, 2020 19:48

  Here is another issue ticket for issues related to this bug: https://github.com/broadinstitute/gatk/issues/6533

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• 

  ABours

  • April 27, 2020 15:23

  Hi,

  I just saw that this bug has been fixed in the 4.1.7.0 version of GATK. So, I was affected by this in 2 out of my 200 samples. I'm now wondering whether I can combinegvcf 198 samples run in haplotypecaller from 4.1.6.0 with the 2 samples run with haplotypecaller of 4.1.7.0?

  I just want to save myself the pain of rerunning everything in the new version, thus I hope you have a satisfying answer to this.

  Best,

  Andrea

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  Bhanu Gandham

  • April 29, 2020 15:52

  Hi ABours

   

  I am not sure what the consequences of combining the v4.1.6.0 and v4.1.7.0 will be on your final results since we have not run such tests on our end. We recommend that you rerun the 2 samples. 

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  ABours

  • April 29, 2020 16:01

  Hi Bhanu,

  Thank you for you reply.

  It's a bit sad, but just to ensure I'll rerun everything in v4.1.7.0.

  Best,

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  rickberon

  • October 19, 2020 07:10

  This is generally the exception to throw if the invocation is illegal because of the state of the receiving object. It signals that a method has been invoked at an illegal or inappropriate time. In other words, the Java environment or Java application is not in an appropriate state for the requested operation. for ex. , in case of java.util.List collection, we use next() method of the ListIterator interface to traverse through the java.util.List. If we call the remove() method of the ListIterator interface before calling the next() method then this exception will be thrown as it will leave the List collection in an unstable state.

   

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