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Error with mixcr analyze -OassemblingFeatures [CDR1,CDR2,CDR3] #540

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dahjan opened this issue Sep 12, 2019 · 4 comments

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@dahjan
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commented Sep 12, 2019

Output

Exception in thread "main" picocli.CommandLine$ExecutionException: Error while running command (com.milaboratory.mixcr.cli.CommandAnalyze$CommandAmplicon@79b9dfcd): java.lang.ArrayIndexOutOfBoundsException: 0
at picocli.CommandLine.execute(CommandLine.java:1004)
at picocli.CommandLine.access$900(CommandLine.java:142)
at picocli.CommandLine$RunLast.handle(CommandLine.java:1199)
at com.milaboratory.mixcr.cli.Main$1.handle(Main.java:72)
at com.milaboratory.mixcr.cli.Main$1.handle(Main.java:61)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:1075)
at com.milaboratory.mixcr.cli.Main.handleParseResult(Main.java:85)
at com.milaboratory.mixcr.cli.Main.main(Main.java:55)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
at com.milaboratory.core.sequence.AbstractArraySequence.codeAt(AbstractArraySequence.java:45)
at com.milaboratory.core.sequence.NucleotideSequence.codeAt(NucleotideSequence.java:30)
at com.milaboratory.mixcr.basictypes.ClonalSequence.getStretches(ClonalSequence.java:88)
at com.milaboratory.mixcr.basictypes.ClonalSequence.isCompatible(ClonalSequence.java:152)
at com.milaboratory.mixcr.basictypes.ClonalSequence.isCompatible(ClonalSequence.java:104)
at com.milaboratory.mixcr.assembler.CloneClusteringStrategy.canAddToCluster(CloneClusteringStrategy.java:55)
at com.milaboratory.mixcr.assembler.CloneClusteringStrategy.canAddToCluster(CloneClusteringStrategy.java:40)
at com.milaboratory.core.clustering.Clustering.performClustering(Clustering.java:179)
at com.milaboratory.mixcr.assembler.CloneAssembler.runClustering(CloneAssembler.java:299)
at com.milaboratory.mixcr.assembler.CloneAssemblerRunner.run(CloneAssemblerRunner.java:124)
at com.milaboratory.mixcr.cli.CommandAssemble.run1(CommandAssemble.java:200)
at com.milaboratory.cli.ACommandWithSmartOverwrite.run0(ACommandWithSmartOverwrite.java:118)
at com.milaboratory.cli.ACommand.run(ACommand.java:90)
at com.milaboratory.mixcr.cli.CommandAnalyze.run0(CommandAnalyze.java:656)
at com.milaboratory.cli.ACommand.run(ACommand.java:90)
at picocli.CommandLine.execute(CommandLine.java:996)

Command

mixcr analyze amplicon -s hsa --starting-material rna --5-end no-v-primers --3-end c-primers --adapters adapters-present --receptor-type BCR --only-productive --align '-OreadsLayout=Unknown' --assemble '-OassemblingFeatures=[CDR1,CDR2,CDR3]' --export '-aaFeature CDR1 -nFeature CDR1 -aaFeature CDR2 -nFeature CDR2 -aaFeature CDR3 -nFeature CDR3 -aaFeature VGene -cGenes -count' prefix.fasta analysis_name

@PoslavskySV

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commented Sep 12, 2019

Thanks for reporting! Could you try this with the latest MiXCR version?

@dahjan

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commented Sep 12, 2019

Thanks for the quick response!

Unfortunately, the same error is observed, and only the first line is ever so slightly different.

Output

Exception in thread "main" picocli.CommandLine$ExecutionException: Error while running command (com.milaboratory.mixcr.cli.CommandAnalyze$CommandAmplicon@77984827): java.lang.ArrayIndexOutOfBoundsException: 0

MiXCR version:

mixcr --version
MiXCR v3.0.10 (built Wed Sep 11 23:40:55 CEST 2019; rev=64a8f48; branch=release/v3.0.10; host=Dmitrys-MBP)
RepSeq.IO v1.3.2 (rev=3bb2070)
MiLib v1.11 (rev=f9219a0)
Built-in V/D/J/C library: repseqio.v1.5

@dbolotin

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commented Sep 12, 2019

Hi Jan,

Please post exact commands you used starting from the align action. Are you using built-in VDJC library?

Can you share the dataset to reproduce the error on our side? (if so, you can write me at bolotin (dot) dmitriy (at) gmail (dot) com )

@dahjan

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commented Sep 12, 2019

Thanks Dmitry, I sent you an email.

Yes, I am using the built-in VDJC library.

As additional information, the MiXCR breaks during the clustering step. It only fails, however, when setting assemblingFeatures to [CDR1,CDR2,CDR3]. For all other combinations (i.e. [CDR1,CDR3], [CDR2,CDR3], [CDR3]) it works fine.

@dbolotin dbolotin closed this in 74125e9 Sep 12, 2019
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