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Unknown weight type: cell. #951

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github-wow opened this issue Jan 7, 2023 · 0 comments
Open

Unknown weight type: cell. #951

github-wow opened this issue Jan 7, 2023 · 0 comments

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@github-wow
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github-wow commented Jan 7, 2023

Hi,

I do:

mixcr postanalysis individual \
*.clns \
pa.individual.json.gz \
--default-downsampling count-reads-auto \
--default-weight-function cell \
--only-productive \
--drop-outliers \
--chains TRA \
--metadata metadata.tsv \
--tables pa.individual.tsv

I see:

Running for chain=TRA
picocli.CommandLine$ExecutionException: Error while running command individual java.lang.IllegalArgumentException: Unknown weight type: cell. Available types: none, default, read, UMI
        at com.milaboratory.mixcr.cli.Main.mkCmd$lambda-21(Main.kt:323)
        at picocli.CommandLine.execute(CommandLine.java:2088)
        at com.milaboratory.mixcr.cli.Main.main(Main.kt:76)
Caused by: java.lang.IllegalArgumentException: Unknown weight type: cell. Available types: none, default, read, UMI
        at com.milaboratory.mixcr.postanalysis.ui.PostanalysisParameters.parseWeightFunction(PostanalysisParameters.java:209)
        at com.milaboratory.mixcr.postanalysis.ui.PostanalysisParameters$MetricParameters.weightFunction(PostanalysisParameters.java:90)
        at com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual$CDR3MetricsParameters.getGroup(PostanalysisParametersIndividual.java:208)
        at com.milaboratory.mixcr.postanalysis.ui.PostanalysisParametersIndividual.getGroups(PostanalysisParametersIndividual.java:78)
        at com.milaboratory.mixcr.cli.postanalysis.CommandPaIndividual.run(CommandPaIndividual.kt:50)
        at com.milaboratory.mixcr.cli.postanalysis.CommandPa.run0(CommandPa.kt:326)
        at com.milaboratory.mixcr.cli.postanalysis.CommandPa.run0(CommandPa.kt:311)
        at com.milaboratory.mixcr.cli.MiXCRCommand.run(MiXCRCommand.kt:42)
        at com.milaboratory.mixcr.cli.MiXCRCommandWithOutputs.run(MiXCRCommandWithOutputs.kt:67)
        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 picocli.CommandLine.execute(CommandLine.java:2078)
        ... 1 more

Here cell is mentioned.

@github-wow github-wow changed the title Unknown weight type: cell. "--default-weight-function": errors Jan 7, 2023
@github-wow github-wow changed the title "--default-weight-function": errors Unknown weight type: cell. Jan 7, 2023
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