text: user734: I have 2 .csv files that contains a list of accession codes. For example for this experiment a .csv file will contain:
  SAMN10870244
  SAMN10870243
  SAMN10870242
  SAMN10870241
  SAMN10870240
  SAMN10870239
  SAMN10870238
  SAMN10870237
  SAMN10870236
  SAMN10870235
  SAMN10870234
  SAMN10870233
  
  Then I run the following 
  for i in $(cat *.csv); do echo ${i}; /usr/bin/sratoolkit/bin/fastq-dump --gzip ${i} & done
  
  
  Some of my downloads takes a lot of time days. Is there a faster way to get stuff from NCBI?
  Are there mirrors of NCBI to accelerate the process?
  Why is it so slow? 
  
  
  user4500: You can try wget to download SRA files from NCBI server. This seems to be 2x faster in terms of CPU time than prefetch and has the advantage of not clogging your /home/ncbi/public/sra/ directory in case you have space limitation. The tutorial for wget downloading method is available at https://github.com/johanzi/ncbi_tutorial.
  Here my timing of the prefetch method:
  time prefetch SRR3300113
  real    3m5.609s
  user    0m6.332s
  sys     0m2.076s
  
  Versus the wget method:
  time wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR330/SRR3300113/SRR3300113.sra
  real    3m4.696s
  user    0m0.456s
  sys     0m3.332s
  
  That makes a user+sys time of 8.402s for prefetch and 3.788s for wget. Not so much difference for real time though (about a second).
  
  user939: Answers to this question can be found on biostars. To give you a short summary:
  
  Faster way might be to use the parallel-fastq-dump, as suggested in this answer. I never tested that tool though, my own experience is that prefetch is more stable than fastq-dump command.
  In that same post it seems that the Japanese mirror seems faster, don't know if that is still valid.
  The reason this is never optimized might be that downloading from SRA is not a task you'll have to do repeatedly, as described here in this post.
  
  
original_text: 734: <p>I have 2 .csv files that contains a list of accession codes. For example for this <a href="https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&amp;from_uid=520914" rel="nofollow noreferrer">experiment</a> a .csv file will contain:</p>
  
  <pre><code>SAMN10870244
  SAMN10870243
  SAMN10870242
  SAMN10870241
  SAMN10870240
  SAMN10870239
  SAMN10870238
  SAMN10870237
  SAMN10870236
  SAMN10870235
  SAMN10870234
  SAMN10870233
  </code></pre>
  
  <p>Then I run the following </p>
  
  <pre><code>for i in <span class="math-container">$(cat *.csv); do echo $</span>{i}; /usr/bin/sratoolkit/bin/fastq-dump --gzip ${i} &amp; done
  </code></pre>
  
  <ol>
  <li>Some of my downloads takes a lot of time days. Is there a faster way to get stuff from NCBI?</li>
  <li>Are there mirrors of NCBI to accelerate the process?</li>
  <li>Why is it so slow? </li>
  </ol>
   4500: <p>You can try <code>wget</code> to download SRA files from NCBI server. This seems to be 2x faster in terms of CPU time than <code>prefetch</code> and has the advantage of not clogging your <code>/home/ncbi/public/sra/</code> directory in case you have space limitation. The tutorial for <code>wget</code> downloading method is available at <a href="https://github.com/johanzi/ncbi_tutorial" rel="nofollow noreferrer">https://github.com/johanzi/ncbi_tutorial</a>.</p>
  
  <p>Here my timing of the <code>prefetch</code> method:</p>
  
  <pre><code>time prefetch SRR3300113
  real    3m5.609s
  user    0m6.332s
  sys     0m2.076s
  </code></pre>
  
  <p>Versus the <code>wget</code> method:</p>
  
  <pre><code>time wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR330/SRR3300113/SRR3300113.sra
  real    3m4.696s
  user    0m0.456s
  sys     0m3.332s
  </code></pre>
  
  <p>That makes a user+sys time of 8.402s for <code>prefetch</code> and 3.788s for <code>wget</code>. Not so much difference for real time though (about a second).</p>
   939: <p>Answers to this question can be found on <a href="https://www.biostars.org/p/91885/" rel="noreferrer">biostars</a>. To give you a short summary:</p>
  
  <ol>
  <li><p>Faster way might be to use the <code>parallel-fastq-dump</code>, as suggested in this <a href="https://www.biostars.org/p/91885/#300457" rel="noreferrer">answer</a>. I never tested that tool though, my own experience is that <code>prefetch</code> is more stable than <code>fastq-dump</code> command.</p></li>
  <li><p>In that same post it seems that the Japanese mirror seems faster, don't know if that is still valid.</p></li>
  <li><p>The reason this is never optimized might be that downloading from <code>SRA</code> is not a task you'll have to do repeatedly, as described here in this <a href="https://www.biostars.org/p/91885/#91895" rel="noreferrer">post</a>.</p></li>
  </ol>
  