text: user4595: 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?
  
  user73: 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
  
  
original_text: 4595: <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>
   73: <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>
  