Error while running command exportClones: While adding VEndTrimmed error: Wrong position value
FreundLab-Michal opened this issue · comments
FreundLab-Michal commented
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
Hi, can you please try using the latest develop version. It seems like a bug that we have just fixed.
FreundLab-Michal commented
great, it works! thank you!