I ran cellranger multi on a TotalSeq B dataset and got this error

[error] Pipestance failed. Error log at:

Log message:
There were not enough reads to auto detect the chemistry: Sample CITE_2 in "/scratch/palmer/E222532_PR_Run01_051222/outs/fastq_path/AAAVFT3HV"
Note that you can avoid auto detection by specifying the specific chemistry type and version.
- Minimum number of required reads = 10000
- Number of reads available = 1408

I'm not sure what to specify the chemistry as. Does anyone know what it might be for CITEseq as part of TotalSeq B? Alternatively, can I reduce the minimum number of required reads?

Thank you

  • 2
    $\begingroup$ The read count looks too low for single cell data. Where are you getting your reads from? $\endgroup$
    – gringer
    Mar 7, 2023 at 18:27

1 Answer 1


I don't think you can reduce the number of reads required for autodetection, and it would be a bad idea anyway, because the guess could go wrong.

From 10X Q&A:

TotalSeq B is specifically designed to be compatible with the Single Cell 3’ v3 and 3.1 workflows

And from CellRanger support:

--chemistry     Optional. Assay configuration. NOTE: by default the assay configuration is detected automatically, which is the recommended mode. You should only specify chemistry if there is an error in automatic detection. Select one of:

    auto for auto-detection (default),
    threeprime for Single Cell 3′,
    fiveprime for Single Cell 5′,
    SC3Pv2 for Single Cell 3′ v2,
    SC3Pv3 for Single Cell 3′ v3,
    SC3Pv3LT for Single Cell 3′ v3 LT,
    SC3Pv3HT for Single Cell 3′ v3 HT,
    SC5P-PE for Single Cell 5′ paired-end (both R1 and R2 are used for alignment),
    SC5P-R2 for Single Cell 5′ R2-only (where only R2 is used for alignment).
    SC3Pv1 for Single Cell 3′ v1. NOTE: this mode cannot be auto-detected. It must be set explicitly with this option.
    ARC-v1 for analyzing the GEX portion of multiome data. NOTE: this mode cannot be auto-detected.

That leaves more than one possible chemistry option that could be applicable to your data. Check with the people who prepared the library if you don't know which library kit was used.


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