how to get fastq file from cellranger?

Question

[Info.shi]

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.

[GenoMax]

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

[Info.shi]

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.

[swbarnes2]

How big are the Undetermined files?

[Info.shi]

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

[swbarnes2]

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

[Info.shi]

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

[GenoMax]

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?

[Info.shi]

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.

[GenoMax]

Run QC metrics: null

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