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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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cellranger count-error fetching fastq file #49

Closed Chenmengpin closed 10 months ago

Chenmengpin commented 4 years ago

Hi everyone,

I'm trying to run 'cellranger count' pipline to get the counts output data using the following code:

cellranger count --id=pbmc \ --fastqs=/mnt/c/Users/dell/scRNA/run_cellranger_count/pbmc_1k_v3_fastqs \ --sample=pbmc \ --transcriptome=/mnt/c/Users/dell/scRNA/run_cellranger_count/refdata-cellranger-GRCh38-3.0.0

But sadly got this error: "Error fetching io for 1923: no such file or directoryChecking sample info..."

It seems like unable to find the fastq files in the given directory, but it certainly does have the files, as the ls commend return the files name and it dose have all the fastq files needed:

DESKTOP-1T8GAGA:/mnt/c/Users/dell/scRNA/run_cellranger_count$ ls pbmc pbmc_1k_v3 pbmc_1k_v3_fastqs refdata-cellranger-GRCh38-3.0.0

So I'm wondering what's wrong with the scripts or any tiny details that I missed. Thank you !

batalha23 commented 2 years ago

I hope you were able to solve the issue in the meantime, but in case it can be helpful for someone else out there: I believe the issue is your input for argument '--sample', it needs to match the sample name in the fastq files. It appears that you are using the tutorial files provided by 10x, and in that case the sample name should be 'pbmc_1k_v3'.