cellranger error message

Question

[Alivia]

I am trying to run cellranger multi on a set of data, but I am getting this error message:

Requested sample(s) not found in fastq directory "/project/obesity/Multiome_scRNA/RabhiN_PHHGEX_L1_ds.184bc144f4e04350a77f8a912c4b266f/"

Available samples: RabhiN_PHHGEX

I am thinking it probably has something to do with how I am naming things, specifically my samples. I had to make custom CMOs, so I'm thinking that could also be part of the issue.

This is my configuration csv:

This is the CMO csv file:

I followed the naming conventions for my files, here is one of the fastq directories for example:

Any suggestion on what I should change?

[GenoMax]

You have not said what kind of files these are but are you following the format for the config file as noted here: https://www.10xgenomics.com/support/software/cell-ranger/latest/advanced/cr-multi-config-csv-opts

[Alivia]

The first is my multi config csv file, the second is my cmo set csv, the last is a directory of fastq files. I have also tried making a sample barcode csv and I still get the same issue. I am following the format given in the link.

[Max]

I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!

[Max]

I'm having a similar issue. The sample_id matches the filename prefix before _S1_L001, but I get the error: Log message: Requested sample(s) not found in fastq directory. Available samples: Pool