endikaprieto

I run the latest develop version, but the pipeline stops in the QC step and reports the attached errors. [R-MIXCR_sample1.179010.out.txt](https://github.com/user-attachments/files/20210279/R-MIXCR_sample1.179010.out.txt) [R-MIXCR_sample1.179010.err.txt](https://github.com/user-attachments/files/20210280/R-MIXCR_sample1.179010.err.txt) [script_1.slurm.txt](https://github.com/user-attachments/files/20210281/script_1.slurm.txt)

docker run --rm \ -e MI_LICENSE="E-VRKEGFHFHNBQIFCUJZOTZPNQISODMMGKRROTCOLBAOTTAOKA" \ -v /mnt/petasan_immuno/raw_data/public/braun_et_al/tcrb:/raw:ro \ -v /mnt/bioinfnas/immuno/eprieto/mixcr/sample1:/work \ ghcr.io/milaboratory/mixcr/mixcr:4.7.0-169-develop \ mixcr analyze generic-amplicon-with-umi \ --species hsa \ --assemble-clonotypes-by CDR3 \ --export-productive-clones-only \ --rna \ -f...

Eliminating this line works. I am just trying to replicate the steps they took to get the exact counts table used in the paper: https://github.com/Wu-Lab-DFCI-Harvard/bulkrhTCR_Script

Here is the [link to the paper](https://www.nature.com/articles/s41586-024-08507-5). Looking at it, could you explain why they are doing this? On GitHub, they indicate the '--tag-pattern '^(R1:) (UMI:N{7}:) R2:' option, meaning the...