Mixcr postanalysis overlap

[singhd6]

Hi, I ran a commnad for postanalysis overlap with the following code in mixcr/4.7.0 and the results files are 1kb in size,


-> i further ran the following code for generating the v gen usage plot

then i received the following error: [singhd6@cc-dclrilog62 BCR_SEQUENCING_DS_REANALYSIS]$ mixcr exportPlots vUsage \

--color-key group \
"/mnt/beegfs/singhd6/Divya_data/vhseq/mixcr_analysis/BCR_SEQUENCING_DS_REANALYSIS//result.json.gz" \

--family-usage
"/mnt/beegfs/singhd6/Divya_data/vhseq/mixcr_analysis/BCR_SEQUENCING_DS_REANALYSIS/plots/vUsage.svg"
Please copy the following information along with the stacktrace:
Version: 4.7.0; built=Wed Aug 07 15:19:48 EDT 2024; rev=976ba14139; lib=repseqio.v5.1
OS: Linux
Java: 11.0.9
Abs path: /mnt/beegfs/singhd6/Divya_data/vhseq/mixcr_analysis/BCR_SEQUENCING_DS_REANALYSIS
Cmd args: exportPlots vUsage --color-key group /mnt/beegfs/singhd6/Divya_data/vhseq/mixcr_analysis/BCR_SEQUENCING_DS_REANALYSIS//result.json.gz --family-usage /mnt/beegfs/singhd6/Divya_data/vhseq/mixcr_analysis/BCR_SEQUENCING_DS_REANALYSIS/plots/vUsage.svg
picocli.CommandLine$ExecutionException: Error while running command vUsage java.lang.NullPointerException
at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$lambda-17(SourceFile:420)
at picocli.CommandLine.execute(CommandLine.java:2088)
at com.milaboratory.mixcr.cli.Main.execute(SourceFile:105)
at com.milaboratory.mixcr.cli.Main.main(SourceFile:101)
Caused by: java.lang.NullPointerException
at com.milaboratory.mixcr.postanalysis.PostanalysisResult.forGroup(SourceFile:68)
at com.milaboratory.mixcr.cli.postanalysis.CommandPaExportPlotsGeneUsage.run(SourceFile:82)
at com.milaboratory.mixcr.cli.postanalysis.CommandPaExport.run0(SourceFile:61)
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$lambda-32(SourceFile:539)
at picocli.CommandLine.execute(CommandLine.java:2078)
... 2 more
[singhd6@cc-dclrilog62 BCR_SEQUENCING_DS_REANALYSIS]$
[singhd6@cc-dclrilog62 BCR_SEQUENCING_DS_REANALYSIS]$
I checked the metadata files it is correctly formatted, could the error be because of the .jason file, also, I want to export the shared clonotype results and v gene usage for each clonotype

[singhd6]

one more issues i am having is:

Index 2 out of bounds for length 2
i checked everything but to my knowledge cant figure the error

[singhd6]

my metadata file for multiple dataset is:
sample group
A2-SUBJ066-IgM_S9_L001.clns IgM
A3-SUBJ018-IgM_S17_L001.clns IgM
B1-SUBJ027-IgG-A_S2_L001.clns IgG
C2-SUBJ053-IgM_S11_L001.clns IgM

[mizraelson]

Was it solved? I see you have generated the plot in #1874