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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
https://mixcr.com
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Error while running command exportClones: While adding VEndTrimmed error: Wrong position value #1510

Closed FreundLab-Michal closed 10 months ago

FreundLab-Michal commented 10 months ago

Expected Result

Export all 27663 clones with mutations information to tsv file

Actual Result

Exported only 3073 clones and stopped with an error

Exact MiXCR commands and error

Version: 4.6.0; built=Sat Dec 09 21:48:42 IST 2023; rev=c9fafa41fe; lib=repseqio.v4.0
        OS: Mac OS X
      Java: 21.0.1
  Cmd args: exportClones --drop-default-fields -cloneId -readCount -uniqueTagCount Molecule -vHit -dHit -jHit -cHit -aaFeature CDR3 -nLength CDR3 -aaLength CDR3 -allNMutations -allAAMutations HD11_S5_L001.clns ../Sequences/HD11.tsv
picocli.CommandLine$ExecutionException: Error while running command exportClones java.lang.IllegalArgumentException: While adding VEndTrimmed error: Wrong position value: -4
    at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$lambda-12(SourceFile:395)
    at picocli.CommandLine.execute(CommandLine.java:2088)
    at com.milaboratory.mixcr.cli.Main.main(SourceFile:101)
Caused by: java.lang.IllegalArgumentException: While adding VEndTrimmed error: Wrong position value: -4
    at com.milaboratory.o.FM.a(SourceFile:75)
    at com.milaboratory.o.ur.a(SourceFile:1586)
    at com.milaboratory.o.ur.b(SourceFile:1480)
    at com.milaboratory.o.ur.b(SourceFile:1468)
    at com.milaboratory.o.uc.invoke(SourceFile:1701)
    at com.milaboratory.o.lt.extractValue(SourceFile:1216)
    at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:583)
    at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:582)
    at com.milaboratory.o.lE.a(SourceFile:25)
    at com.milaboratory.o.mp.put(SourceFile:40)
    at cc.redberry.pipe.CUtils.drain(CUtils.java:82)
    at cc.redberry.pipe.util.PipeExtensionsKt.drainToAndClose(PipeExtensions.kt:155)
    at com.milaboratory.mixcr.cli.CommandExportClones$Cmd.run1$runExport(SourceFile:322)
    at com.milaboratory.mixcr.cli.CommandExportClones$Cmd.run1(SourceFile:369)
    at com.milaboratory.mixcr.cli.MiXCRCommandWithOutputs.run0(SourceFile:69)
    at com.milaboratory.mixcr.cli.MiXCRCommand.run(SourceFile:37)
    at picocli.CommandLine.executeUserObject(CommandLine.java:1939)
    at picocli.CommandLine.access$1300(CommandLine.java:145)
    at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
    at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)
    at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)
    at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
    at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)
    at com.milaboratory.mixcr.cli.Main.registerLogger$lambda-27(SourceFile:514)
    at picocli.CommandLine.execute(CommandLine.java:2078)
    ... 1 more

When trying to export without the mutations data, it works well.

Defult setting of ExportClones tsv file - HD11_S5_L001.clones_IGH.tsv.zip Short file with mutations - HD11_IGH.tsv.zip cln file - HD11_S5_L001.clns.zip Assemble report - HD11_S5_L001.assemble.report.txt

Michal

mizraelson commented 10 months ago

Hi, can you please try using the latest develop version. It seems like a bug that we have just fixed.

FreundLab-Michal commented 10 months ago

great, it works! thank you!