text: user900: I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem related to this issue. Since according to the entry, AWS S3 also hosts the original BAM files, I thought I could download these directly.
  Example SRA Entry
  
  NCBI documentation implies that I can't download this directly, but I can freely copy to other AWS locations within the region. To this end, I created my own S3 bucket (mm-mneuron) and am now trying to copy from the SRA bucket to mine.  Here's what I try:
  import boto3
  import botocore
  
  s3 = boto3.resource('s3')
  
  bam_file = {
    'Bucket': 'sra-pub-src-6',
    'Key': 'SRR5253957/RPI25_0.bam'
  }
  
  my_bucket = s3.Bucket('mm-mneuron')
  
  my_bucket.copy(bam_file, 'RPI25_0.bam')
  
  This fails with:
  
  botocore.exceptions.ClientError: An error occurred (403) when calling
    the HeadObject operation: Forbidden
  
  That is, it sounds like I can't access the SRA bucket. I've tested downloading and uploading to my bucket, so I know I have write permissions. Not sure what else to try here.
  How can I access the SRA data on S3? 
  
  user900: A member of the SRA submission staff pointed out that using
  prefetch --type all SRR5253957
  
  will download the original files. In this case, it means running the above within an EC2 instance colocated with the S3 bucket (so, us-east-1) and having installed and configured SRA Toolkit to work from AWS (as per this documentation).
  Unfortunately, the particular files I am concerned with are not currently accessible, but this should generically work in most situations.
  
original_text: 900: <p>I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use <code>sam-dump</code>, but the files are having issues that seem related to <a href="https://github.com/ncbi/sra-tools/issues/23" rel="nofollow noreferrer">this issue</a>. Since according to the entry, AWS S3 also hosts the original BAM files, I thought I could download these directly.</p>
  
  <h2>Example SRA Entry</h2>
  
  <p><img src="https://i.stack.imgur.com/LP8Y7.png" alt="enter image description here"></p>
  
  <p>NCBI documentation implies that I can't download this directly, but I can freely copy to other AWS locations within the region. To this end, I created my own S3 bucket (<code>mm-mneuron</code>) and am now trying to copy from the SRA bucket to mine.  Here's what I try:</p>
  
  <pre><code>import boto3
  import botocore
  
  s3 = boto3.resource('s3')
  
  bam_file = {
    'Bucket': 'sra-pub-src-6',
    'Key': 'SRR5253957/RPI25_0.bam'
  }
  
  my_bucket = s3.Bucket('mm-mneuron')
  
  my_bucket.copy(bam_file, 'RPI25_0.bam')
  </code></pre>
  
  <p>This fails with:</p>
  
  <blockquote>
    <p>botocore.exceptions.ClientError: An error occurred (403) when calling
    the HeadObject operation: Forbidden</p>
  </blockquote>
  
  <p>That is, it sounds like I can't access the SRA bucket. I've tested downloading and uploading to my bucket, so I know I have write permissions. Not sure what else to try here.</p>
  
  <p><strong>How can I access the SRA data on S3?</strong> </p>
   900: <p>A member of the SRA submission staff pointed out that using</p>
  
  <pre><code>prefetch --type all SRR5253957
  </code></pre>
  
  <p>will download the original files. In this case, it means running the above within an EC2 instance colocated with the S3 bucket (so, <strong>us-east-1</strong>) and having installed and configured SRA Toolkit to work from AWS (<a href="https://www.ncbi.nlm.nih.gov/sra/docs/sra-aws-download/" rel="nofollow noreferrer">as per this documentation</a>).</p>
  
  <p>Unfortunately, the particular files I am concerned with are not currently accessible, but this should generically work in most situations.</p>
  