CellRanger - No input FASTQs were found for the requested parameters

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2.1 years ago

shuaizh117 ▴ 10

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."

Cellranger FASTQ • 1.2k views

ADD COMMENT • link 2.1 years ago by shuaizh117 ▴ 10

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Are your files not gzipped? Possibly that's the problem.

ADD REPLY • link 2.1 years ago by swbarnes2 14k

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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!

ADD REPLY • link 2.1 years ago by shuaizh117 ▴ 10

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