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ERROR: No input FASTQs were found for the requested parameters. #246

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2124sa opened this issue May 11, 2024 · 1 comment
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ERROR: No input FASTQs were found for the requested parameters. #246

2124sa opened this issue May 11, 2024 · 1 comment

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@2124sa
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2124sa commented May 11, 2024

I am grateful for your assistance. I am a novice in using cellranger. While executing cellranger count, I encountered an error. Below is the error message.
ERROR: No input FASTQs were found for the requested parameters.

If your files came from bcl2fastq or mkfastq:

  • Make sure you are specifying the correct --sample(s), i.e. matching the sample sheet
  • Make sure your files follow the correct naming convention, e.g. SampleName_S1_L001_R1_001.fastq.gz (and the R2 version)
  • Make sure your --fastqs points to the correct location.
  • Make sure your --lanes, if any, are correctly specified.
    Refer to the "Specifying Input FASTQs" page at https://support.10xgenomics.com/ for more details.

My code is cellranger count --id=bc --transcriptome=/home/a2433564374/public/cellranger.index/refdata-gex-GRCh38-2024-A --fastqs=/home/a2433564374/lesson/lesson1-cellranger/out --create-bam=true --sample=bc --nosecondary

I am utilizing the version 8.0.0 of CellRanger

(cellranger1) a2433564374@lizhengjian:/public/cellranger.index$ ls
refdata-gex-GRCh38-2024-A refdata-gex-GRCh38-2024-A.tar.gz
(cellranger1) a2433564374@lizhengjian:
/public/cellranger.index$ cd refdata-gex-GRCh38-2024-A
(cellranger1) a2433564374@lizhengjian:/public/cellranger.index/refdata-gex-GRCh38-2024-A$ ls
fasta genes reference.json star
(cellranger1) a2433564374@lizhengjian:
/public/cellranger.index/refdata-gex-GRCh38-2024-A$ pwd
/home/a2433564374/public/cellranger.index/refdata-gex-GRCh38-2024-A

(cellranger1) a2433564374@lizhengjian:/lesson/lesson1-cellranger$ cd out
(cellranger1) a2433564374@lizhengjian:
/lesson/lesson1-cellranger/out$ ls
bc_S1_LOO1_R1_001.fastq.gz bc_S1_LOO1_R2_001.fastq.gz
(cellranger1) a2433564374@lizhengjian:~/lesson/lesson1-cellranger/out$ pwd
/home/a2433564374/lesson/lesson1-cellranger/out

How should I proceed to address this issue? Once again, I express gratitude for your assistance!

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Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail [email protected] for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.

@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale May 11, 2024
@github-actions github-actions bot locked and limited conversation to collaborators May 11, 2024
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