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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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better error message than "Formatting error in sample sheet" #134

Closed slowkow closed 8 months ago

slowkow commented 2 years ago

I think we can do better than giving this error:

https://github.com/10XGenomics/cellranger/blob/e6517cae10b030973968dec91e09710063297fde/tenkit/mro/stages/make_fastqs/make_fastqs_preflight_local/__init__.py#L62

I got this error for a _rna_bcl.csv file when I ran cellranger, and it didn't help to find the underlying problem.

So, I manually ran tk_sheet.file_is_simple_samplesheet(csv_path) on my file. Here's what I got:

WARNING:root:Unrecognized sample index: SI-TT-I9
WARNING:root:Unrecognized sample index: SI-TT-I10
WARNING:root:Unrecognized sample index: SI-TN-D8
WARNING:root:Unrecognized sample index: SI-TN-D9

This is helpful! We can check and see that SI-TT-I9 is not a valid sample index.

Now, I hope my cellranger run will finish without error if I fix this sample index.

It'd be ideal if the original error message would include this information.

davemcg commented 1 year ago

Much appreciated Kamil - I was getting this error and your post helped me realize that it appears the sequencing center gave me the wrong indexes....