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Aragorn Issue

| posted 19 Jun, 2019 13:32
Has anyone been having trouble accessing Aragorn? We have not been able to access it for a couple days now.

| posted 25 Jun, 2019 15:13
I am late to this game, but I have not had any trouble accessing Aragorn.
| posted 25 Jun, 2019 15:32
I get this when trying to go to the Aragorn site: unexpectedly closed the connection.

| posted 25 Jun, 2019 15:41
It won't load for me at all, still. I asked some people to try it at the last SMART meeting, and it didn't load for them either, so there may be something going on. Welkin mentioned she heard there may be a retirement coming up.

| posted 25 Jun, 2019 16:15
It also doesn't load for me. Time to send an email ???
| posted 25 Jun, 2019 16:33
A quick google search suggests that the "ERR_CONTENT_LENGTH_MISMATCH" error is probably an issue with nginx (the web server software) so yes it is time for an email.

I did look for anywhere else that was running public available Aragorn but only found a galaxy server running the older 1.2.36 which does not appear to trim correctly (based on a single prediction in phage saftant that we ran to test).

If anyone is desperate, one can easily install the command line version with conda on mac, or apt-get on ubuntu version 18 or 19. Still looking for a viable web based solution.
Edited 25 Jun, 2019 17:44
| posted 25 Jun, 2019 18:23
OK since we are working on a few phage here, I have installed command line Aragorn ver 1.2.38. If anyone is in a hurry and does not want to wait until web based Aragorn is back up, I can easily run aragorn command line for you, just send me an email with the sequence as a fasta file attachment and I can email back the aragorn results.
| posted 28 Jun, 2019 15:51
I've heard back from Bjorn CAnback— he is aware that the server is down and is working to bring it back online.
| posted 28 Jun, 2019 15:58

Question, though. I caught up on the meeting that I had to leave from yesterday and have a question that pertains to this. Perhaps the new version of the virtual machine could include some of these useful tools all put together? The new Starterator from Chris, a standalone Aragorn in case we loose it in the future (or it's down again, or until we can host it somewhere), the new version of the splitstree prep-program, and the newest version of the checker?

I'd happily upgrade.

| posted 28 Jun, 2019 19:11
Christian and I are working on a version of the VM with the experimental version of starterator in the faculty account as well as k-phamerate for validation and phamnexus for splitstree prep. Unfortunately, there is no easy way to get the newer version of aragorn that trims the genes properly installed on that old Ubuntu 14.04 VM.
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