MiXCR error with the complied cat TCR library
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
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