Comments (3)
Can you confirm the issue still occurs with the latest MiXCR v 4.5?
from mixcr.
Yes, it still occurs.
Please copy the following information along with the stacktrace:
Version: 4.5.0; built=Fri Sep 22 15:39:05 EEST 2023; rev=cdb24b4fb7; lib=repseqio.v3.0.1
OS: Linux
Java: 11.0.13
picocli.CommandLine$ExecutionException: Error while running command align java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$lambda-12(SourceFile:340)
at picocli.CommandLine.execute(CommandLine.java:2088)
at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd$PlanBuilder.executeSteps(SourceFile:478)
at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd.run0(SourceFile:368)
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$lambda-26(SourceFile:447)
at picocli.CommandLine.execute(CommandLine.java:2078)
at com.milaboratory.mixcr.cli.Main.main(SourceFile:98)
Caused by: java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
at java.base/java.util.Collections$SingletonList.get(Collections.java:4849)
at com.milaboratory.o.df.a(SourceFile:3081)
at com.milaboratory.mixcr.cli.CommandAlignPipeline$TagsExtractor.parse(SourceFile:409)
at com.milaboratory.mixcr.cli.CommandAlign$Cmd$run1$lambda-15$$inlined$mapUnchunked$1.process(SourceFile:36)
at cc.redberry.pipe.CUtils.lambda$chunked$2(CUtils.java:182)
at cc.redberry.pipe.util.SimpleProcessorWrapper.take(SimpleProcessorWrapper.java:43)
at cc.redberry.pipe.util.SimpleProcessorWrapper.take(SimpleProcessorWrapper.java:40)
at cc.redberry.pipe.blocks.ParallelProcessor$Worker.run(ParallelProcessor.java:306)
at java.base/java.lang.Thread.run(Thread.java:829)
from mixcr.
Currently we do not support using 10x bam
files, because CELL and UMI tags are saved as separate fields in it and not as a read sequence. We will add such feature in the future, please use FASTQ files with 10x data for now.
from mixcr.
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from mixcr.