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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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The problem of mixcr exportPlots shmTrees #1686

Open WZQ6 opened 1 month ago

WZQ6 commented 1 month ago

When I run commandline with "mixcr exportPlots shmTrees --metadata /home/EXP0033VH/metadata.tsv --node-color sample --line-color sample --node-label sample --alignment-aa CDR3 /home/EXP0033VH/findalle/findshmt/output.shmt /home/EXP0033VH/findalle/findshmt/tree_plot.pdf" I can't get the output results , with the wrong message: Version: 4.6.0-209-develop; built=Thu May 30 18:50:11 CST 2024; rev=015a589864; lib=repseqio.v5.0 OS: Linux Java: 21.0.3 Abs path: /home/EXP0033VH/findalle/findshmt Cmd args: exportPlots shmTrees --metadata /home/EXP0033VH/metadata.tsv --node-color sample --line-color sample --node-label sample --alignment-aa CDR3 /home/EXP0033VH/findalle/findshmt/output.shmt /home/EXP0033VH/findalle/findshmt/tree_plot.pdf picocli.CommandLine$ExecutionException: Error while running command shmTrees java.lang.NullPointerException at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$lambda-17(SourceFile:419) 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.o.wr.a(SourceFile:191) at com.milaboratory.o.wr.a(SourceFile:200) at com.milaboratory.o.wr.a(SourceFile:200) at com.milaboratory.o.wr.a(SourceFile:200) at com.milaboratory.o.wD.invoke(SourceFile:4165) at kotlin.sequences.TransformingSequence$iterator$1.next(Sequences.kt:210) at kotlin.sequences.SequencesKt_SequencesKt.toCollection(Sequences.kt:787) at kotlin.sequences.SequencesKtSequencesKt.toMutableList(_Sequences.kt:817) at kotlin.sequences.SequencesKt___SequencesKt.toList(_Sequences.kt:808) at com.milaboratory.o.wy.a(SourceFile:159) at com.milaboratory.o.wy.invoke(SourceFile:145) at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74) at com.milaboratory.mixcr.cli.CommandExportShmTreesPlots.run1(SourceFile:1145) 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-32(SourceFile:538) at picocli.CommandLine.execute(CommandLine.java:2078) ... 2 more Please help me. Thanks a lot.

mizraelson commented 3 weeks ago

Hi, Is it possible that the metadata and the sample files' names in the output.shmt do not match? Can you share the metadata file and the output.shmt file? You can reach us out at support@milaboratories.com

mizraelson commented 3 days ago

Hi, I wanted to follow up on that. Is the issue still present?