Cellranger count with error information "... which wasn't expected, or isn't valid in this context"

Question

[diqixiaoyaoer]

Hello everyone,

I just practiced the scRNAseq upstream analysis from cellranger official tutorial.

But I met a small problem but it stopped me from going the next step.

I followed the tutorial exactly but the error information still exist:

##
cellranger count --id=run_count_1kpbmcs \
   --fastqs=/home/user/Desktop/run_cellranger_count/pbmc_1k_v3_fastqs \
   --sample=pbmc_1k_v3 \
   --transcriptome= /home/user/Desktop/run_cellranger_count/refdata-gex-GRCh38-2020-A

error: Found argument '/home/user/Desktop/run_cellranger_count/refdata-gex-GRCh38-2020-A' which wasn't expected, or isn't valid in this context

USAGE:
    cellranger count [OPTIONS] --id <ID> --transcriptome <PATH>

For more information try --help

I tried many methods but I didn't know what's wrong with it .

Can somebody help me solve this problem. I'd be appreciate it.

Answer 1

[ATpoint]

Whitespace between transcriptome= and the path /home...

[diqixiaoyaoer]

Oh, yes. I got it. It wasted me mucht time. But I think the problem reason is ridiculous.

I am really thankful for you help.

[Chris]

Hi, I got similar error:

cellranger count --id=run_count --fastqs=/data/sn_mouse \ --transcriptome=/data/sn_mouse/refdata-gex-mm10-2020-A

error: Found argument ' --transcriptome=/sn_mouse/refdata-gex-mm10-2020-A' which wasn't expected, or isn't valid in this context

Would you please have a suggestion?

[ATpoint]

At first remove the espcae \ and see whether it's the additional whitespace in there, then validate that the folder really exists at that path. Is it really /sn_mouse/... which would suggest the folder is in the root directory.

[Chris]

Hi ATpoint, if I remove the \, I got this:

ERROR: No input FASTQs were found for the requested parameters.

I put the fastq files and the folder refdata-gex-mm10-2020-A in the same folder sn_mouse

[ATpoint]

I cannot hands-on debug this for you. Make sure the file paths are correct. Easiest is to cd into the folder with the fastq file and then use pwd to get the path. Make sure this is all correct. It seems a simple path error.

[Chris]

Thank you for your help. I know it seems a simple error message but I tried all I know. When I change the order --fastq to the end of the command, I got:

ERROR: No input FASTQs were found for the requested parameters.

cellranger count --id=run_count --transcriptome=/data/sn_mouse/refdata-gex-mm10-2020-A --fastqs=/data/sn_mouse/fastq/

If I delete a / :

cellranger count --id=run_count --transcriptome=data/sn_mouse/refdata-gex-mm10-2020-A --fastqs=/data/sn_mouse/fastq/

error: Invalid value "data/sn_mouse/refdata-gex-mm10-2020-A" for '--transcriptome <PATH>': No such file or directory. So I think it is not the problem of the path.

At the beginning, I put all fastq file and folder refdata-gex-mm10-2020-A in the same directory sn_mouse. I tried to separate them but still got the error. Same error when running on a .sh file.

Update: I figure it out. The name of the fast file must be exactly as required format on 10x website.