findAlleles with 10x single cell data

[XIA CHENRUI]

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 follow your tutorial on B cell lineage at https://mixcr.com/mixcr/guides/b-cell-lineages-webinar/#quality-control using my 10x single cell VDJ seq data. I could run mixcr analyze 10x-sc-xcr-vdj. But I can not run findAlleles function successfully.

Actual Result

Not sure

Exact MiXCR commands

mixcr findAlleles \               
    --report mixcr_CZC_bcr/DCh.findAlleles.report.txt \
    --export-alleles-mutations mixcr_CZC_bcr/DCh_alleles.tsv \
    --export-library mixcr_CZC_bcr/DCh_alleles.json \
    --output-template {file_dir_path}/{file_name}.reassigned.clns \
    mixcr_CZC_bcr/*.clns

MiXCR report files

App version: 4.6.0; built=Sat Dec 09 19:48:42 UTC 2023; rev=c9fafa41fe; lib=repseqio.v4.0
Some of the inputs were processed by `assembleContigs` or `analyze` without `--assemble-contigs-by` option: mixcr_CZC_bcr/mixcr_CZC_bcr.contigs.clns, mixcr_CZC_bcr/mixcr_CZC_bcr.grouped.clns

[mizraelson]

Please add --assemble-contigs-by VDJRegion to your mixcr analyze command.

This will fix the error.