1mpicocli.CommandLine$ExecutionException: Error while running command align java.lang.IllegalStateException: Single aligner is already set. 1mpicocli.CommandLine$ExecutionException: Error while running command align java.lang.IllegalArgumentException: floating point already set.

[myang02]

Hi! I am looking for some advice/guidance on my code. I have been getting the errors: "Single aligner is already set." and "floating point already set." when I run Mixcr. My files are named in the following format:

VC162_360_P162_103_02_P01_rep1_P_A01_S1_R1_001.fastq.gz

However, I make sure to use wildcard placeholders when running my code:

VC162_360_P162_103_02_P01_rep1_P_A01_{{CELL0ROW:a}}{{CELL0COL:a}}_{{R}}_001.fastq.gz

For each sample that is analyzed the following error(s) come up:

"1mpicocli.CommandLine$ExecutionException: Error while running command align java.lang.IllegalArgumentException: floating point already set"
"1mpicocli.CommandLine$ExecutionException: Error while running command align java.lang.IllegalStateException: Single aligner is already set."

Is there something wrong with the way I am naming my files or writing code?

This is the line of code for reference ('FastqFile_Mixcr4_Syntax' refers to both R1 and R2 files with the wildcard naming syntax):
mixcr -Xmx100g analyze smart-seq2-vdj --species hsa "${FastqFile_Mixcr4_Syntax}" "${analysisFilePath}/${each_sampleNAME}"

Thank you!

[mizraelson]

Hi, could you try using the latest version: https://link.milaboratory.com/software/mixcr/mixcr-develop.zip