align java.lang.IllegalArgumentException: floating point already set

[KoenDeserranno]

Checklist before submitting the issue:

• The issue is strongly related to the MiXCR software
• The issue can be reproduced with the most recent version of MiXCR
• There is no answer to the question in the official documentation and there is no duplicate issue in the bug tracker
• Inspection of raw alignments with exportAlignmentsPretty shows that data has the expected architecture, and sample preparation artefacts are not the reason of the problem (if this is the matter of the issue)

Expected Result

I am currently running MiXCR (4.7.0) on Smart-seq3 data, however I am not successful to start the alignment process from paired-end input. The input reads are demultiplexed per cell (R1 and R2.fastq.gz file for each cell). If I only supply the R1.fastq.gz file as /demultiplexed_fastq/{{CELL:a}}_R1.fastq.gz, and adapt the --tag-pattern accordingly ( "^ATTGCGCAATG(UMI:N{12})GGG(R1:*)", MiXCR does work.

Actual Result

However, I am getting the error: picocli.CommandLine$ExecutionException: Error while running command align java.lang.IllegalArgumentException: floating point already set

Exact MiXCR commands

mixcr analyze generic-lt-single-cell-fragmented-with-umi --species mmu --rna --assemble-contigs-by VDJRegion -t 20 --tag-pattern "^ATTGCGCAATG(UMI:N{12})GGG(R1:*)\^(R2:*)" /demultiplexed_fastq/{{CELL:a}}_R1.fastq.gz /demultiplexed_fastq/{{CELL:a}}_R2.fastq.gz result

Thanks for the help!

[mizraelson]

Hi, can you please try the following command:

mixcr analyze generic-lt-single-cell-fragmented-with-umi --species mmu --rna --assemble-contigs-by VDJRegion -t 20 --tag-pattern "^ATTGCGCAATG(UMI:N{12})GGG(R1:*)\^(R2:*)" /demultiplexed_fastq/{{CELL:a}}_{{R}}.fastq.gz result

[KoenDeserranno]

Thank you for the swift reply! Unfortunately, I now have a slightly different error

java -jar ./mixcr.jar analyze generic-lt-single-cell-fragmented-with-umi --species mmu --rna --assemble-contigs-by VDJRegion -t 8 --tag-pattern "^ATTGCGCAATG(UMI:N{12})GGG(R1:*)\^(R2:*)" ./demultiplexed_fastq/{{CELL:a}}_{{R}}.fastq.gz result

Command line output:

>>>>>>>>>>>>>>>>>>>>>>> mixcr align <<<<<<<<<<<<<<<<<<<<<<<
Running:
mixcr align --report result.align.report.txt --json-report result.align.report.json --threads 8 --preset generic-lt-single-cell-fragmented-with-umi --save-output-file-names result.align.list.tsv --rna --species mmu --tag-pattern ^ATTGCGCAATG(UMI:N{12})GGG(R1:*)\^(R2:*) --assemble-contigs-by VDJRegion ./demultiplexed_fastq/{{CELL:a}}_{{R}}.fastq.gz result.alignments.vdjca
The following tags and their roles will be associated with each output alignment:
  Payload tags: R1, R2
  Cell tags: CELL(NS)
  Molecule tags: UMI(SQ)
Alignment: 0%
Please copy the following information along with the stacktrace:
   Version: 4.7.0-233-develop; built=Tue Sep 09 20:44:49 CEST 2025; rev=71e897a137; lib=repseqio.v6.3
        OS: Linux
      Java: 17.0.11-internal
  Abs path: /home/tools/MiXCR
  Cmd args: align --report result.align.report.txt --json-report result.align.report.json --threads 8 --preset generic-lt-single-cell-fragmented-with-umi --save-output-file-names result.align.list.tsv --rna --species mmu --tag-pattern ^ATTGCGCAATG(UMI:N{12})GGG(R1:*)\^(R2:*) --assemble-contigs-by VDJRegion /demultiplexed_fastq/{{CELL:a}}_{{R}}.fastq.gz result.alignments.vdjca

picocli.CommandLine$ExecutionException: Error while running command align java.lang.IllegalStateException: Single aligner is already set.

[mizraelson]

Hi, can you try removing all the files and running the command again I tried the same exact one and it didn't return any errors.

[KoenDeserranno]

Thanks for the reply!
I installed MiXCR again from conda on a new machine, and ran the same command. However, I keep getting the floating point error ... Any other ideas?

`
mixcr analyze generic-lt-single-cell-fragmented-with-umi --species mmu --rna --assemble-contigs-by VDJRegion -t 20 --tag-pattern "^ATTGCGCAATG(UMI:N{12})GGG(R1:)^(R2:)" /fastq_demux/{{CELL:a}}_{{R}}.fastq.gz result

Running:
mixcr align --report result.align.report.txt --json-report result.align.report.json --threads 20 --preset generic-lt-single-cell-fragmented-with-umi --save-output-file-names result.align.list.tsv --rna --species mmu --tag-pattern ^ATTGCGCAATG(UMI:N{12})GGG(R1:)^(R2:) --assemble-contigs-by VDJRegion /fastq_demux/{{CELL:a}}{{R}}.fastq.gz result.alignments.vdjca
The following tags and their roles will be associated with each output alignment:
Payload tags: R1, R2
Cell tags: CELL(NS)
Molecule tags: UMI(SQ)
Alignment: 0%
WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.google.common.cache.Striped64 (file:/home/share/mixcr-4.7.0-0/mixcr.jar)
WARNING: Please consider reporting this to the maintainers of class com.google.common.cache.Striped64
WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
Please copy the following information along with the stacktrace:
Version: 4.7.0; built=Wed Aug 07 21:19:48 CEST 2024; rev=976ba14139; lib=repseqio.v5.1
OS: Linux
Java: 24.0.2-internal
Abs path: /home/
Cmd args: align --report result.align.report.txt --json-report result.align.report.json --threads 20 --preset generic-lt-single-cell-fragmented-with-umi --save-output-file-names result.align.list.tsv --rna --species mmu --tag-pattern ^ATTGCGCAATG(UMI:N{12})GGG(R1:)^(R2:) --assemble-contigs-by VDJRegion /fastq_demux/{{CELL:a}}{{R}}.fastq.gz result.alignments.vdjca
picocli.CommandLine$ExecutionException: Error while running command align java.lang.IllegalArgumentException: floating point already set
at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$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.CommandAnalyze$Cmd$PlanBuilder.executeSteps(SourceFile:543)
at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd.run0(SourceFile:444)
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$lambda-32(SourceFile:539)
at picocli.CommandLine.execute(CommandLine.java:2078)
at com.milaboratory.mixcr.cli.Main.execute(SourceFile:105)
at com.milaboratory.mixcr.cli.Main.main(SourceFile:101)
Caused by: java.lang.IllegalArgumentException: floating point already set
at com.milaboratory.o.DN.a(SourceFile:6099)
at com.milaboratory.o.Eb.e(SourceFile:66)
at com.milaboratory.mixcr.vdjaligners.VDJCAligner.d(SourceFile:109)
at com.milaboratory.o.Ef.e(SourceFile:54)
at com.milaboratory.mixcr.vdjaligners.VDJCAligner.d(SourceFile:109)
at com.milaboratory.mixcr.cli.CommandAlign$Cmd$run1$lambda-24$$inlined$mapChunksInParallel$1.process(SourceFile:1071)
at cc.redberry.pipe.CUtils.lambda$chunked$2(CUtils.java:182)
at cc.redberry.pipe.blocks.ParallelProcessor$Worker.run(ParallelProcessor.java:308)
at java.base/java.lang.Thread.run(Thread.java:1447)
`

[mehdiborji-takeda]

I observed the warning you are seeing (WARNING: A terminally deprecated method in sun.misc.Unsafe has been called) when I did fresh install of MiXCR where it automatically installed a very new version of java (25 with release in Sep or Oct last year). I'm not sure if I ran into your bug, but the pipeline kept going out of memory because some of memory leak.

My issue was resolved by downgrading the java.

[mizraelson]

@KoenDeserranno The bug has been fixed in the recent develop version.

[mizraelson]

@mehdiborji-takeda The Warning you see is indeed due to the Java version, but it shouldn't lead to OOM. If you still have the error text and the command you run please share and I will take a look!

[mehdiborji-takeda]

@mizraelson Thank you for your response. I ran did this Sep or Oct of last year on a server I don't have access to anymore.
But the command was mixcr analyze 10x-sc-5gex --species hsa, applied to VDJ enriched fastqs of the following 10x public datasets:
https://www.10xgenomics.com/datasets/human-b-cells-from-a-healthy-donor-post-flu-vaccination-v-2-2-standard-5-0-0
https://www.10xgenomics.com/datasets/human-b-cells-from-a-healthy-donor-pre-flu-vaccination-v-2-2-standard-5-0-0