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how to get fastq file from cellranger?

Hi everyone I am new to single cell analysis

I need to create fastq file from BCL

My code in bash file look like-

cd /project/shikhasi/project/apps/cellranger-6.1.2/cellranger mkfastq --id=20_10x \
--run=/project/yard/20_10x/2_BHHNTLDRXY \
--csv=/project/yard/20_10x/cellranger-20210813_10x-bcl-simple-1.2.0.csv

But I can't able to get out file I make sure the the directory of my file but still it is not working.

Could anyone please help me out.

Any suggestion will highly appreciated.

cellranger mkfastq
• 2,794 views • link
updated by GenoMax GenoMax • written by Info.shi • Info.shi

Are you getting an error? cellranger requires an install of Illumina bcl2fastq. Have you installed that?

• 0 views • link
written by GenoMax GenoMax

No I don't get error and yes I already installed cellranger and bcl2fastq even I notification on my terminal its successful

like this

**Outputs:

  • Run QC metrics: null
  • FASTQ output folder: /project/outs/fastq_path
  • Interop output folder: /project/outs/interop_path
  • Input samplesheet: /project/outs/input_samplesheet.csv Waiting 6 seconds for UI to do final refresh. Pipestance completed successfully!**

But when I see directory ../outs/fastq_path/HHNTLDRXY there are several folder but its all empty. Kindly please suggest me.

Thank you.

• 0 views • link
written by Info.shi • Info.shi

How big are the Undetermined files?

• 0 views • link
written by swbarnes2 swbarnes2

Hi thanks for your reply Undermined files is not created in my directory

• 0 views • link
written by Info.shi • Info.shi

The should be somewhere. Maybe a level or two out.

• 0 views • link
written by swbarnes2 swbarnes2

The problem is I can’t able to generate fastq files in out/ fast_path directory which is empty folder where I expected fastq file even in that folder and even undetermined files is not created but it’s like I successfully run cell ranger

• 0 views • link
written by Info.shi • Info.shi

You will need to find the cellranger log file and check in there to see what is happening. While you may have installed bcl2fastq is it in your $PATH?

• 0 views • link
written by GenoMax GenoMax

Thank you for helping me I checked my log file seems like okay

In the end it looks like this

**Outputs:

  • Run QC metrics: null
  • FASTQ output folder: /project/outs/fastq_path
  • Interop output folder: /project/outs/interop_path
  • Input samplesheet: /project/outs/input_samplesheet.csv 2022-12-16 18:12:24 [perform] Serializing pipestance performance data. Waiting 6 seconds for UI to do final refresh. Pipestance completed successfully! 2022-12-16 18:12:30 Shutting down. 2022-12-16 18:12:30 [jobmngr] Highest memory usage observed: { "rss": 487694336, "shared": 21696512, "vmem": 2487250944, "text": 9900032, "stack": 2115936256, "proc_count": 52 }**

Thank you.

• 0 views • link
written by Info.shi • Info.shi

Run QC metrics: null

This means the error is somewhere upstream in that file. Please check the entire file.

• 0 views • link
written by GenoMax GenoMax

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