Hello, 

I am trying to analyze the public dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126030
I've downloaded the fastq files onto my cluster, and would like to proceed with cellranger count. 

I am in a test folder and the only file is: SRR8526547_1.fastq and refdata-cellranger-GRCh38-1.2.0


    cellranger count --id=cellranger \
                     --transcriptome=/home/jl2/scratch60/refdata-cellranger-GRCh38-1.2.0/ \
                     --fastqs=.\
                     --sample=SRR8526547_1.fastq \


I keep getting the error of 

    Invalid path/prefix combination: /gpfs/ycga/scratch60/k/jl2/test, ['SRR8526547_1.fastq']
    No input FASTQs were found for the requested parameters.

Can't seem to figure out what's wrong. Does it need fastq.gz instead of fastq? 


Hello,

I have been troubleshooting
> error: No input FASTQs were found for the requested parameters.

for several hours now. In my case the file names, the file path and the command were all fine. Finally what solved the issue for me was to move the fastq.gz files into a seperate folder that only contained fastq.gz files. The original folder had some other files in it (md5, fastqc output, etc.). Not sure why this was a problem for the pipeline, but make sure to give this a try if you run into similar trouble.

Best,
Max