CellRanger - No input FASTQs were found for the requested parameters
Hello! Can anyone help with the problem of "No input FASTQs were found for the requested parameters" using CellRanger 6.1.2?
My FASTQ files are saved to the path: /home/zhaos/beegfs/shuai/FASTQ/ and are named like:
GC.SZ.1060_1_S1_L001_I1_001.fastq
GC.SZ.1060_1_S1_L001_R1_001.fastq
GC.SZ.1060_1_S1_L001_R2_001.fastq
GC.SZ.1060_1_S1_L002_I1_001.fastq
GC.SZ.1060_1_S1_L002_R1_001.fastq
GC.SZ.1060_1_S1_L002_R2_001.fastq
The code I use is as below:
cellranger count --id=test --fastqs=/home/zhaos/beegfs/shuai/FASTQ/ --sample=GC.SZ.1060_1 --transcriptome=/home/zhaos/beegfs/yard/run_cellranger_count/refdata-gex-GRCh38-2020-A/
It keeps giving me ERROR: "ERROR: No input FASTQs were found for the requested parameters."
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shuaizh117 •
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Are your files not gzipped? Possibly that's the problem.
I figured it out. Cellranger doesn't allow any dot in the sample name, so I changed GC.SZ.1060 to GCSZ1060 and issue solved. Thanks tho!