@fhsantanna I think this data is hidden from some accounts, and when you contact GISAID, they fix it on their end.
It is very frustrating. I sent two emails, the first one was sent almost one month ago, and I had no response.
How long did they take to give you a feedback?
Same problem for me, files dont show up on my account. I tried the account of a colleague with the same problem.
So far I have no reply from GISAID.
If someone has recent context data for EUROPE, please write me a message to caspar.gross@med.uni-tuebingen.de
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Hi all. I had this problem too and here’s a quick note on my experience.
After emailing about the issue using the contact page on gisaid.org, I was contacted by the person who handles support in my time zone. The issue somehow had to do with me having two emails registered under my name. When he removed the defunct account (that I forgot existed), the download modal was complete when I logged back in. No idea how these two issues are related, but cleaning up my account solved it.
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Hi folks,
I recently had this issue as well, but when I reached out to GISAID I got the following response:
Following a growing number of user requests to offer file formats that are compatible across a variety of tools, and mindful of evolving variants of concern around the globe, a section ‘Download packages’ was created to offer users more current and a larger variety of data packages. If you are already using a pipeline, you may only need to update the header, and you’re good to go.
It sounds like GISAID is not hosting nextfasta and nextmeta files anymore, is this correct?
Hi @fshepherd. Looking now, there is a new section in the GISAID website called “Download packages” that includes “FASTA” and “metadata”.
However, this metadata file is slightly different than what’s expected by the Nextstrain ncov workflow (with “Location” being things like “Oceania / Australia / Northern territory”).
That said, the section “Genomic epidemiology” still lists the entry point files “FASTA” and “metadata” for me:
This leads me to believe that if you’re not seeing this “Genomic epidemiology” section it’s an issue specific to your account. Maybe try writing again and requesting access to these specific files? I’m not sure what fraction of users are encountering this issue.
Ah good to know, I do see some files under that the genomic epidemiology heading but not the fasta/metadata. I will ask them again, with the right file names this time. Thanks for taking the time to respond!
Thanks for following up @fshepherd. The absence of “FASTA” and “metadata” under “Genomic epidemiology” seems to exist for a number of other users as well. I’m following up with GISAID to see what might be going on here.
I’m also having the same issue, have asked for access through the contact form (4 days ago) but no response. Have just emailed hCoV-19@gisaid.org today, to request access. Will update if still nothing 
I suspect I am having the same account issues as others, but where is the “download packages” section of the website? This is what I can see… is that what you are talking about?
Hi @trvrb I’ve been having this issue with the data too! I asked GISAID for access to the genomic epidemiology versions but they told me that I can use the download packages fasta + metadata for the Augur / Auspice tool. But… it’s not working
These guys?
What happens?
I was able to run against them, but am uncertain if they were the same dataset as recommended in the example.
So, I have got it running with the region-specific auspice files. I’ll stick to that! I’m so confused with all the different data versions I don’t know what works or doesn’t work anymore!
There aren’t that many sequences in these files…
My guess(!!!) is that these are pre-sampled in a way that provides enough context to view other sequences in a global or regional context. On the other hand if one were doing proximity sampling that information is lost… I’m a little suspicious of what I’m seeing in the results from that build. For the moment I’m just using the files to get familiar with the process and hope I hear back from gisaid :/.
Huzzah! I got access to the data. I had written several time, but what worked was sending the community build, explain what I wanted to do (write an article) and explain why the current data wasn’t working… unclear canonical background dataset for that region of the world, lack of ability to (conveniently) find descendants for the purposes of travel surveillance… and just not wanting to miss anything if preventing results in any form. One of those hit for them, I suppose… the access was changed in a few hours.
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