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.