Answers.Body: <p>Run align-info  to see the references used.
  Run prefetch &lt;/path/to/sra/file&gt; to download missed references.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-03-07T14:49:17.370Z
Answers.LastActivityDate: 2022-03-07T14:49:17.370Z
Answers.UserDisplayName: Dan Bolser
Body: <p><em>Note: this question was also asked on <a href="https://github.com/ncbi/sra-tools/issues/202" rel="nofollow noreferrer">Github</a>.</em></p>
  <p>I have 241 SRA files that appear to be reference compressed. I didn't even know this was a thing until I tried to convert them to Fastq files without an internet connection. I got the &quot;name not found while resolving...&quot; error described at the bottom of <a href="https://ncbi.github.io/sra-tools/fastq-dump.html" rel="nofollow noreferrer">this page</a> when I attempted to do the conversion.</p>
  <p>The instructions say:</p>
  <blockquote>
  <p><em>If you have elected to prevent the toolkit from contacting NCBI, you will need to manually acquire the reference(s) here</em></p>
  </blockquote>
  <p>We have many NCBI databases mirrored locally, including RefSeq, so it's likely that we already have all the references. I have two questions:</p>
  <ul>
  <li>How do I determine the reference used to compress a reference-compressed SRA file? (Note this needs to be scripted for 241 SRA files, so manual inspection is out of the question.)</li>
  <li>Once I've determined the correct reference and ensured it is available locally, how to I tell <code>fastq-dump</code> where to find it?</li>
  </ul>
  
Tags: <file-formats><fastq><format-conversion><sratoolkit>
Title: Determine reference for reference-compressed SRA file
ThreadText: # Determine reference for reference-compressed SRA file
  
  (Asked by: username_0 on 2019-05-14)
  
  *Note: this question was also asked on [Github](https://github.com/ncbi/sra-tools/issues/202).*
  
  I have 241 SRA files that appear to be reference compressed. I didn't even know this was a thing until I tried to convert them to Fastq files without an internet connection. I got the "name not found while resolving..." error described at the bottom of [this page](https://ncbi.github.io/sra-tools/fastq-dump.html) when I attempted to do the conversion.
  
  The instructions say:
  
  > *If you have elected to prevent the toolkit from contacting NCBI, you will need to manually acquire the reference(s) here*
  
  We have many NCBI databases mirrored locally, including RefSeq, so it's likely that we already have all the references. I have two questions:
  
  * How do I determine the reference used to compress a reference-compressed SRA file? (Note this needs to be scripted for 241 SRA files, so manual inspection is out of the question.)
  * Once I've determined the correct reference and ensured it is available locally, how to I tell `fastq-dump` where to find it?
  
  **Tags:** file-formats, fastq, format-conversion, sratoolkit
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-03-07. Score: 1
  
  Run align-info to see the references used.
  Run prefetch </path/to/sra/file> to download missed references.
  
  
  ---
  
  