Warn when no FastQ files available from ENA

[vang42]

Bash script for downloading FastQ files just keeps on spinning and produces no script. Is ENA down or changed or..?

[ewels]

It's working fine for me.. What are the accessions that you're trying to fetch?

Can you see any Javascript errors in your browser console? (See step 3 in this page)

[vang42]

no, no errors. I am trying to fetch SRP162370

[ewels]

It looks like the ENA doesn't have FastQ files for this project: https://www.ebi.ac.uk/ena/data/view/PRJNA489865

You'll have to download the SRA files and convert them yourself I'm afraid.

Phil

[ewels]

Looking at the results from the ENA (eg. here), I guess I should be able to flag to the user that no FastQ files were returned for a given SRA object.

[ewels]

I should also catch and warn erroneous http responses, such as 505.. A few crop up for me semi-randomly when I query a lot of accessions.