Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-06T09:38:14.880Z
Answers.LastActivityDate: 2021-05-06T09:38:14.880Z
Answers.UserDisplayName: gringer
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-06T08:00:49.543Z
Comments.Text: 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.
Comments.UserDisplayName: fra
Tags: <single-cell><bash><linux><10x-genomics><cellranger>
Title: Cellranger gives error
ThreadText: # 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.  
  
  ---
  
  ## 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](https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/count#header)). 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
  
  ```
  
  
  ---
  
  