error: The subcommand 'mkref --genome=GRCh38' wasn't recognized Did you mean 'mkref'? If you believe you received this message in error, try re-running with 'cellranger -- mkref --genome=GRCh38

[QianRongAn]

Stranger problem, this morning, my command is "cellranger count --id=HRR572954 --transcriptome=refdata-cellranger-GRCh38-1.2.0 --fastqs=/data1/肝癌单细胞GSA数据-HCC --sample=HRR572954",received respond is : ERROR: No space left on device, so then I deleted some samples In the afternoon, I found the command "cellranger" can't be recognize： it must be add "./" in the front the I add it received respond seems the reference is not indexed: So I use the command "mkref" but I remember to have already build the index, then I received the stranger mistake: error: The subcommand 'mkref --genome=GRCh38' wasn't recognized Did you mean 'mkref'? If you believe you received this message in error, try re-running with 'cellranger -- mkref --genome=GRCh38

[QianRongAn]

Incidentally, I realised the environment variable maybe disappear and my supposed was right, but another blocks is environment variables can't be configured and the reasons are confused. This morning, I wanna try again and there is no "base" environment, it's successfully configured and imput "cellranger" directly can be recognised, no longer need "./" in the front. And I run "count" command again, it's hint the reference doesn't be indexed, I use "mkref" command then back to the original question here:( The subcommand 'mkref --genome=GRCh38' wasn't recognized

[QianRongAn]

I use command:

cellranger -- mkref --genome=GRCh38 \
                --fasta=Homo_sapiens.GRCh38.dna.primary_assembly.fa \
                --genes=Homo_sapiens.GRCh38.84.filtered.gtf \
                --ref-version=1.2.0

still same error above.

[QianRongAn]

I ues another method to write command like this:

cellranger mkref --genome=GRCh38 --fasta=Homo_sapiens.GRCh38.dna.primary_assembly.fa --genes=Homo_sapiens.GRCh38.84.filtered.gtf

And this command is runing unexpectedly received "Reference successfully created!" BUT the 'count' command still saying my reference doesn't appear to be indexed :(

[QianRongAn]

someone told me I can use the build-in genome, no need indexed the reference, she shared the code below: cellranger count --id=HRR572950 --transcriptome=refdata-gex-GRCh38-2020-A --fastqs=/data1/liver-cancer-GSA-HCC --sample=HRR572950 this code is useful and solve my problem. this code is different from the previous one is the parameter "--transcriptome", I think that I read the wrong tutorial in the Internet.