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!

[Julian]

This was my problem as well even though I am not using custom CMO's. The documentation should be improved on this part, as it is unclear that you need to change "gex1" (standard template) or "mux1" to the name of your fastq sample name, in your case "RabhiN_PHHGEX".

[libraries]
fastq_id,fastqs,feature_types
mux1,/project/....,Multiplexing....

Needs to be:

[libraries]
fastq_id,fastqs,feature_types
RabhiN_PHHGEX,/project/....,Multiplexing....

[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