data not uploading

usegalaxy.eu support
1

Hi, for some reason I can’t upload BAM files today - the upload seems to get stuck around 10%. I have tried a few files and all have the same issue, which I haven’t had before. Is there an issue with the server?
thanks

2

Hi @Imran_Noorani

We are reviewing! Thanks for reporting the problem and more feedback soon. :hammer_and_wrench:

3

Hi @Imran_Noorani

To confirm: if this was at UseGalaxy.org, could you please try again now?

If this was at UseGalaxy.eu – I also had a BAM file that was stalling from a local upload, but not when loading via URL. We can look into this more if needed, please let us know.

And if you want to, you can check what your internet “up” speed is. That is how much data you can transfer to somewhere else.

A search with something like “speed test” will usually give some options for wherever you happen to be located. You can try comparing runs when at different locations/times since this can vary quite a bit. The Galaxy servers can accept data quickly but only as fast as your side is able to provide it.

4

Hi @jennaj

thanks it is the .org site. I just tried again and the BAM stops uploading at 5%. It’s not our speed as i use the Institute’s server which is super fast and have loaded to other servers yesterday without. issues. I wonder if there is an issue at the Galaxy end, as it was uploading fine until 2 days ago? I also tried different browsers…

thanks

5

Hi @Imran_Noorani

I tested a ~ 500 MB file yesterday a few times (also a BAM) and it worked in several accounts. So I’m wondering if there is anything special about your BAM file and how you are loading it, and maybe where you are loading the data. My tests were at UseGalaxy.org.

If you are loading by locally browsing the file: once the process starts, you can close the Upload modal and the progress will display in the far left side behind the “Upload” icon. You can also click on that icon to open the dialogue box again.

More tips:

  1. Which browser you use shouldn’t matter, but we do recommend Safari, Chrome, and Firefox for best performance with Galaxy overall.
  2. To check which server you are using, see the URL at the top of your browser window.
  3. Use default settings, then update the tags or database assignment after. You can use the “guess” from Galaxy to confirm that the data loading worked correctly.
  4. Large data transfers will take longer. The connection needs to stay active. That means you will need to stay logged into your account for the duration.
  5. If the file is on storage attached to your computer, maybe try moving the file to your computer first, then Upload from there. (this is a corner case but seems worth mentioning since you are at work and this might be what is going on – that other storage location is not sending data well for some reason?)
  6. If all else fails, you can try using the method described here → GitHub - galaxyproject/galaxy-upload: Galaxy Upload Utility for the CLI
  7. Hosting the data on a service where you can load by URL is also an option. That could be another Galaxy server: if you are located in the EU, you could load to UseGalaxy.eu (if that is working for you?), then move the data between servers by URL? FAQ: Transfer entire histories from one Galaxy server to another
  8. Help summary guide → Getting Data into Galaxy

Hope this helps, and you can share more details.

6

Hi thanks. I tried the EU galaxy server on Friday after moving the file to my computer first and uploading from there which worked. However I tried the same today on both Galaxy versions and unfortunately the BAMs fail to upload again. I think there is an issue with your server?
thanks

7

now works on EU server - it says they had a power failure earlier today!

1 Like
8

Ok, great, thanks for the update @Imran_Noorani !!

I had trouble loading data there too last week. Glad it is resolved now. :rocket: