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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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IndexOutOfBoundsException: Index 2 out of bounds for length 2 #1836

Closed pursellta closed 3 weeks ago

pursellta commented 3 weeks ago

I ma trying to run the non-enriched 10x VDJ pipeline with a custom reference. I have successfully used the custom reference before. I downloaded the fastqs from SRA and am running the pipeline with a sample sheet. Here is the command and associated error: Version: 4.7.0; built=Wed Aug 07 12:19:48 PDT 2024; rev=976ba14139; lib=repseqio.v5.1 OS: Linux Java: 11.0.13 Abs path: /home/tpursell/bats/Arjam_Flu_10x/SRA_Files/arjam_WT_intestine_9dpi Cmd args: analyze 10x-sc-5gex -t 20 --species ajam --library Arjam-IG-V1.json.gz --assemble-contigs-by VDJRegion --split-by-sample /home/tpursell/bats/Arjam_Flu_10x/SRA_Files/arjam_WT_intestine_9dpi/Arjam_intestine_9dpi.tsv /home/tpursell/bats/Arjam_Flu_10x/SRA_Files/arjam_WT_intestine_9dpi/mixcr.bcr.20241025/

picocli.CommandLine$ExecutionException: Error while running command analyze java.lang.IndexOutOfBoundsException: Index 2 out of bounds for length 2 at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$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.IndexOutOfBoundsException: Index 2 out of bounds for length 2 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248) at java.base/java.util.Objects.checkIndex(Objects.java:372) at java.base/java.util.ArrayList.get(ArrayList.java:459) at com.milaboratory.mixcr.presets.FullSampleSheetParsed$Companion$parse$parsedRows$1$inputIdx$1.invoke(SourceFile:320) at com.milaboratory.mixcr.presets.FullSampleSheetParsed$Companion$parse$parsedRows$1$inputIdx$1.invoke(SourceFile:320) at com.milaboratory.mixcr.presets.FullSampleSheetParsed$Companion.put(SourceFile:262) at com.milaboratory.mixcr.presets.FullSampleSheetParsed$Companion.parse(SourceFile:320) at com.milaboratory.mixcr.presets.FullSampleSheetParsed$Companion.parse(SourceFile:271) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd$inputSampleSheet$2.invoke(SourceFile:289) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd$inputSampleSheet$2.invoke(SourceFile:287) at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd.getInputSampleSheet(SourceFile:287) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd.access$getInputSampleSheet(SourceFile:96) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd$inputFileGroups$2.invoke(SourceFile:297) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd$inputFileGroups$2.invoke(SourceFile:295) at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd.getInputFileGroups(SourceFile:295) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd.validate(SourceFile:313) at com.milaboratory.mixcr.cli.MiXCRCommand.run(SourceFile:35) 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

pursellta commented 3 weeks ago

It was a problem with the sample sheet.