mixcr downsampling

[atiwariliverpool]

I am trying to run mixcr downsample for my sample (single cell - 10x platform) but receive this error please help

mixcr downsample --chains TRB --downsampling random:1000 --only-productive --summary A004_downsample_summary.tsv --suffix _downsampled --out A004-Hu-NPTX2-TETpos-CD8-1D-TCR_S7_downsampled A004-Hu-NPTX2-TETpos-CD8-1D-TCR_S7.clna
IMPORTANT: MiXCR will use at most 6212MB of RAM,
use -Xmx to change automatically set heap size (i.e. -Xmx50g to set heap size to 50 Gb)
Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/scratch
4.3.2; built=Tue Apr 11 11:35:07 PDT 2023; rev=123d699964; lib=repseqio.v2.2
picocli.CommandLine$ExecutionException: Error while running command downsample java.lang.ArrayIndexOutOfBoundsException: 1
at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$lambda-13(SourceFile:322)
at picocli.CommandLine.execute(CommandLine.java:2088)
at com.milaboratory.mixcr.cli.Main.main(SourceFile:102)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 1
at com.milaboratory.mixcr.postanalysis.ui.DownsamplingParameters.parse(SourceFile:102)
at com.milaboratory.mixcr.cli.postanalysis.CommandDownsample.run1(SourceFile:135)
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-27(SourceFile:430)
at picocli.CommandLine.execute(CommandLine.java:2078)
... 1 more

[mizraelson]

Hi, there are several types of downsampling that are described here.

For example, if you want to downsample to a 1000 randomly selected reads use:

--downsampling count-reads-fixed-1000