As I run the Cellranger count, I get the following error: "The argument '--fastqs <PATH>...' requires a value but none was supplied"

Question

I am following the 10x Cellranger steps and using the same files for cellranger count. I run this from the fastq directory that contains all the PBMCs fastq files and the GRCh38 files too.

Answer 1

You put a space between --fastqs= and /home/.../pbmc_1k_v3_fastqs, and thus it think you didn't provide an argument after --fastqs. There are two possible syntax:

• either you want a space, but then don't put a =, as in --fastqs /home/.../pbmc_1k_v3_fastqs;
• or you put an equal sign, but then don't put a space, as in --fastqs=/home/.../pbmc_1k_v3_fastqs.