I have never had problems transferring FASTQ files from EBI to my galaxy site. Beginning last week, I have been unable to transfer SRR772111. I have successfully transferred this in the past. I get inconsistent error messages including site unavailable and trouble with decompressing, and sometimes the transfer just runs without completing.
This is the reponse I received from the EBI folks to my inquiry - the problem will hopefully be resolved by next week :))
"On 2017.01.06., at 13:50, Marc Rossello firstname.lastname@example.org wrote:
The problems with the FTP servers that were limiting data downloads (or transferring files to Galaxy) have now largely been resolved and connections can be made and data downloaded. We are expecting the service to be stable by EOB today. It is still in an "at-risk" condition and the performance could be slower than usual until the beginning of next week.
Sorry for the inconvenience.
There are currently issues with data retrieval from EBI SRA, their technical team is working on fixing it.
In the meantime, you can use NCBI SRA Tools for SRA data retrieval. See this post about importing paired end data with NCBI SRA Tools.
Hope this helps!
Been having the same problem for a few weeks. I tried the SRA Tools but the workflows consistently resulted in errors when I tried this. Have resorted to downloading the files to my computer and then uploading them to Galaxy via an FTP server. Does anyone have a better solution?