cellranger count error "Your reference does not contain the expected files, or they are not readable. Please check your reference folder on n145"

Question

[leranwangcs]

I downloaded the cell ranger reference database from wget https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0.tar.gz then I tar tar xvzf the .tar.gz file and got a refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 folder in my path.

But when I run the cell ranger count command, I got an error said: [error] Your reference does not contain the expected files, or they are not readable. Please check your reference folder on n145.

I have deleted and reinstalled the databased several times but still got the same error. Can anybody provide me some advice on this please?

Thank you very much!

[GenoMax]

Can you provide the complete command you are trying to use? Which specific cellranger program are you using?

[leranwangcs]

Yeah I should have, Sorry about that! Here is my command:

cellranger count --id=run_count_BAAK-FCW-FW099J --transcriptome=/scratch/mtblab/leran/scRNA_seq/ref/refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 --fastqs=/scratch/mtblab/leran/scRNA_seq/data --sample=BAAK-FCW-FW099J-1A-1,BAAK-FCW-FW099J-1A-2,BAAK-FCW-FW099J-1B,BAAK-FCW-FW099J-2A,BAAK-FCW-FW099J-2B-1,BAAK-FCW-FW099J-2B-2

Thanks very much!!

[ylws2201]

Maybe, you should check your cellranger version, and makesure the ref was made by the right cellranger version.

Answer 1

[yjk122123]

It looks to me that you downloaed the VDJ reference instead of the reference for GEX data? Since you used ""cellranger count", I assume the fastq files you have contains GEX data. Otherwise, you might want to try "cellranger vdj".

Answer 2

[leranwangcs]

To answer myself's question: I used a vdj database for my gene expression data. So when I switch to the correct databases, it worked.