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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

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exportClones error with Imputed

Angieiscute opened this issue · comments

commented

Hi,
I'm using the following command:
mixcr exportClones -o -t --chains TRB -nFeatureImputed V5UTRGermline -nFeatureImputed L1 -nFeatureImputed L2 alignment.clns result.tsv
However, it results in an error message as follows:

Exporting clones: 0%
Exporting clones: 11.8% ETA: 00:00:07
Exporting clones: 29.9% ETA: 00:00:03
java.lang.AssertionError:
[{false 0 123 150}, {true 1 47 51}, {false 1 0 2}]
[{false 0 123 150}, {true 0 47 51}]
91441
at com.milaboratory.o.jO.m(SourceFile:588)
at com.milaboratory.o.BB.a(SourceFile:98)
at com.milaboratory.o.BB.a(SourceFile:105)
at com.milaboratory.o.jO.j(SourceFile:372)
at com.milaboratory.o.rB.invoke(SourceFile:1370)
at com.milaboratory.o.kQ.extractValue(SourceFile:55)
at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:316)
at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:315)
at com.milaboratory.o.kW.a(SourceFile:25)
at com.milaboratory.o.lv.put(SourceFile:40)
at com.milaboratory.mixcr.cli.CommandExportClones$Cmd$ExportClones.run(SourceFile:368)
at com.milaboratory.mixcr.cli.CommandExportClones$Cmd.run1$runExport(SourceFile:285)
at com.milaboratory.mixcr.cli.CommandExportClones$Cmd.run1(SourceFile:332)
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-26(SourceFile:447)
at picocli.CommandLine.execute(CommandLine.java:2078)
at com.milaboratory.mixcr.cli.Main.main(SourceFile:98)

However, when I omit the export of the imputed L1 part (by excluding the -nFeatureImputed L1 option), the export is successful.

Do you have any insights into what might be causing this issue with this sample data? BTW, it's mouse data, if I use the human library to analyze the is no problem.

Thanks!

Best,

Angie

commented

Could you please specify the MiXCR version you used and the commands executed before exportClones? It's important to note that to successfully export a particular feature, it needs to be included in the clonotype assembly feature and must be at least partially covered.

I tested your command on 5'RACE data using MiXCR 4.6, employing the --assemble-clonotypes-by VDJTranscript option in the mixcr analyze command, and it functioned as expected.

Sincerely,
Mark

commented

I will close the issue for now, feel free to reopen.