MiXCR error with the complied cat TCR library

Question

[Kaj]

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

Answer 1

[Kaj]

After I carefully read about notice for creating library from IMGT-style padded fasta file, I noticed that I forgot to specify positions of anchor points in D region. After this was corrected, the library worked perfectly.

Answer 2

[akh22]

Hi Kaj,

I hope you will get this message but could you possibly post your json anchor library ? I am trying to do the same for cat Ig and can't find a good example of how to assemble the custom library.

Thanks.