Hello!
I am trying to upload fastq.gz files to usegalaxy.org using the upload tool (up arrow). I was able to upload one however when i tried to upload another i get the following: Warning: Waiting for server to resume…
I tried to ftp connect with filezilla and received an error that it was unable to connect to the server.
I am very new to galaxy and suspect that i am getting an error because i am doing something incorrectly but i am not sure what that is. any help would be appreciated
thank you
For the past two days I have been trying to run jobs that have previously run successfully but they are stuck on various steps (no error, just not progressing). Other people have had problems like mine in the past when there was server issues, so I’m wondering if something is currently wrong with the server…
Thank you for your response; I feel a little less crazy now!
I managed to upload one more fastq.gz file but it is now stuck as well (grey box in history stating: this job is waiting to run).
The Galaxy Main https://usegalaxy.org public server is very, very busy. Some patience will be needed for all operations.
There is also a warning banner at the top of that server specifying certain tools that are running with reduced memory or are temporarily disabled (server resource-related). That banner will update and/or go away as status changes.
For those working at other public Galaxy servers, also experiencing delays, it is expected that most are also very busy. But you can ask them yourself for clarification. Check the home page of the server for contact information or administrative messages. Known public Galaxy server’s also sometimes include contact information in their “Galaxy Platform Directory” listing here: https://galaxyproject.org/use/.
More people are using home internet connections rather than work/university connections – and home connections tend to be optimized for data downloads, not uploads. Running a “speedtest” type of test can help you to determine your own bandwidth (internet search with the keyword “speedtest”). Contact your IP provider to find out about what options are available to increase “the up” speed, the volume of data transfer allowed, and/or if some sites or all sites are blocked and/or what triggers data transfer throttles and/or if they experiencing more load than usual.
What this means in practical terms:
Loading data from your local computer up to anywhere else is almost always going to be slower, for everyone right now, and not just when loading to Galaxy. Whether the file is locally browsed or FTP is used.
Loading data, for anyone, will be slower, due to uploads from everyone else taking longer than usual to complete.
For slower connections, FTP is usually a better choice. Details about transfer progress and the option to resume transfer can be clearer, whether FTP is used line-command or through an FTP client.
If you can, place data on a site that is not local to your home. Load it by URL from that site to Galaxy. Be aware that the URL must be publically accessible. This is still someone private – someone else would have to know that URL to access the data. The data you put at some 3rd site doesn’t need to stay there publically accessible – after loaded to Galaxy (or wherever you are moving it), change permissions or migrate the data out of the public location.
If you are not sure about the privacy requirements for your data, check with the admin/security group you work with. A good idea anyway when moving data around and working with it, to/from/at any public or cloud locations, not just public Galaxy servers.