MiXCR error with the complied cat TCR library

MiXCR error with the complied cat TCR library

0

Dear great helpers,

I compiled json library for cat’s TCR using ‘repseqio’ as attached file. The command lines were as followed:

$MIXCR analyze amplicon 
--threads 20 
--library imgt 
--species "cat" 
--starting-material rna 
--5-end v-primers 
--3-end j-primers 
--adapters adapters-present 
--receptor-type tcr 
--region-of-interest VDJRegion 
--only-productive 
--align "-OreadsLayout=Collinear" 
--assemble "-OseparateByC=true" 
--assemble "-OqualityAggregationType=Average" 
--assemble "-OclusteringFilter.specificMutationProbability=1E-5" 
--assemble "-OmaxBadPointsPercent=0" 
SRR10350408_1.fq SRR10350408_2.fq test.analysis

After testing it with the cat’s TCR miSeq data, I got the error as indicated:

picocli.CommandLine$ExecutionException: Error while running command
(com.milaboratory.mixcr.cli.CommandAnalyze$CommandAmplicon@344344fa):
java.lang.ArrayIndexOutOfBoundsException: Index 19 out of bounds for
length 19
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:76)
at com.milaboratory.mixcr.cli.Main$1.handle(Main.java:65)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:1075)
at com.milaboratory.mixcr.cli.Main.handleParseResult(Main.java:89)
at com.milaboratory.mixcr.cli.Main.main(Main.java:59) Caused by: java.lang.ArrayIndexOutOfBoundsException: Index 19 out of bounds
for length 19
at io.repseq.core.AbstractReferencePoints.getWrappingGeneFeature(AbstractReferencePoints.java:198)
at io.repseq.core.VDJCLibrary.getChecksum(VDJCLibrary.java:89)
at io.repseq.core.VDJCLibrary.getLibraryId(VDJCLibrary.java:206)
at com.milaboratory.mixcr.cli.CommandAlign.getConfiguration(CommandAlign.java:308)
at com.milaboratory.mixcr.cli.CommandAlign.getFullPipelineConfiguration(CommandAlign.java:299)
at com.milaboratory.cli.ACommandWithSmartOverwrite.handleExistenceOfOutputFile(ACommandWithSmartOverwrite.java:76)
at com.milaboratory.cli.ACommandWithOutput.validate(ACommandWithOutput.java:45)
at com.milaboratory.cli.ACommandWithSmartOverwrite.validate(ACommandWithSmartOverwrite.java:61)
at com.milaboratory.mixcr.cli.CommandAlign.validate(CommandAlign.java:382)
at com.milaboratory.mixcr.cli.CommandAnalyze.inheritOptionsAndValidate(CommandAnalyze.java:320)
at com.milaboratory.mixcr.cli.CommandAnalyze.getAlign(CommandAnalyze.java:338)
at com.milaboratory.mixcr.cli.CommandAnalyze.run0(CommandAnalyze.java:668)
at com.milaboratory.cli.ACommand.run(ACommand.java:90)
at picocli.CommandLine.execute(CommandLine.java:996)
… 7 more

Would you please help me fix the issue?

Best regards,
Kaj


repseqio


MiXCR

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