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Note: this question was also asked on Github.

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 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?
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