<p>Two of those command line parameters should be accessible locations (see <a href="https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/count#header" rel="nofollow noreferrer">here</a>). Could you please add the output of the following commands:</p>
<p><code>ls -l /data/fi1d18/Downloads/FASTQ_scATAC/ | head</code></p>
<p>and</p>
<p><code>ls -l refdata-cellranger-arc-GRCh38-2020-A-2.0.0 | head</code></p>
<p>I suspect that the refdata link should be an absolute path, rather than a relative path, i.e. something like this:</p>
<pre><code>cellranger-atac count --id test --reference /opt/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 --fastqs /data/fi1d18/Downloads/FASTQ_scATAC/ --chemistry ARC-v1
</code></pre>

CC BY-SA 4.0
2021-05-06T09:38:14.880Z
2021-05-06T09:38:14.880Z
gringer
<p>I am trying to run cellranger but I get fastq permission denied error</p>
<pre><code>fi1d18@RBGO-Server2:/opt<span class="math-container">$ cellranger-atac count --id test --reference refdata-cellranger-arc-GRCh38-2020-A-2.0.0 --fastqs /data/fi1d18/Downloads/FASTQ_scATAC/ --chemistry ARC-v1
error: couldn't open MRO file
    Caused by: Permission denied (os error 13)
fi1d18@RBGO-Server2:/opt$</span> 
</code></pre>
<p>I have added the path by</p>
<pre><code>export PATH=/opt/cellranger-atac-2.0.0:$PATH
</code></pre>
<p>And by vim I have also added the path</p>
<pre><code>fi1d18@RBGO-Server2:/opt$ vim ~/.bashrc
</code></pre>
<p>Any help please?</p>

CC BY-SA 4.0
2021-05-06T08:00:49.543Z
Does your user have permission to read inside `opt` ? `mro` are configurations files used and read by cellranger during each steps. If they cannot be access, then the pipeline should fail.
fra
<single-cell><bash><linux><10x-genomics><cellranger>
Cellranger gives error
# Cellranger gives error

(Asked by: username_0 on 2021-05-06)

I am trying to run cellranger but I get fastq permission denied error
fi1d18@RBGO-Server2:/opt$ cellranger-atac count --id test --reference refdata-cellranger-arc-GRCh38-2020-A-2.0.0 --fastqs /data/fi1d18/Downloads/FASTQ_scATAC/ --chemistry ARC-v1
error: couldn't open MRO file
    Caused by: Permission denied (os error 13)
fi1d18@RBGO-Server2:/opt$ 

I have added the path by
export PATH=/opt/cellranger-atac-2.0.0:$PATH

And by vim I have also added the path
fi1d18@RBGO-Server2:/opt$ vim ~/.bashrc

Any help please?

**Tags:** single-cell, bash, linux, 10x-genomics, cellranger
> **Comments:**
> **username_1**: Does your user have permission to read inside `opt` ? `mro` are configurations files used and read by cellranger during each steps. If they cannot be access, then the pipeline should fail.  

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## 1 answers

### Answer by username_2 on 2021-05-06. Score: 1 | Accepted answer

Two of those command line parameters should be accessible locations (see here). Could you please add the output of the following commands:
ls -l /data/fi1d18/Downloads/FASTQ_scATAC/ | head
and
ls -l refdata-cellranger-arc-GRCh38-2020-A-2.0.0 | head
I suspect that the refdata link should be an absolute path, rather than a relative path, i.e. something like this:
cellranger-atac count --id test --reference /opt/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 --fastqs /data/fi1d18/Downloads/FASTQ_scATAC/ --chemistry ARC-v1


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