SEA-PHAGES | Locked out of Phamerator

Link to this post \| posted 28 Feb, 2017 16:10
c.sunnen	Hi all, I've had this happen to a couple of students in the last week. In one case, it fixed itself, in the others, we're still encountering the problem. Please note that in all cases, Phamerator was working just fine previously. Upon attempting to open Phamerator, a password is being required that we don't have. We can't even open it without this passkey. The box that pops up says: "Database Setup Required. Paherator needs to set up your database. Please enter your root database password." I know how to change the database, but I can't even access the Edit menu to do so when this happens. Thanks for your help! Nikki

Link to this post | posted 28 Feb, 2017 16:10

Hi all,

I've had this happen to a couple of students in the last week. In one case, it fixed itself, in the others, we're still encountering the problem. Please note that in all cases, Phamerator was working just fine previously.

Upon attempting to open Phamerator, a password is being required that we don't have. We can't even open it without this passkey. The box that pops up says: "Database Setup Required. Paherator needs to set up your database. Please enter your root database password." I know how to change the database, but I can't even access the Edit menu to do so when this happens.

Thanks for your help!

Nikki

Link to this post \| posted 01 Mar, 2017 15:39
DanRussell	Hi Nikki, Did you try "phage" for the password? If phamerator ever wants a password, that's the one. If that doesn't help, Steve recently answered a similar question via email, so I'm going to copy his response here: It sounds like one of two things: your virtual machine is unable to access the internet your phamerator configuration file has become corrupted You can test the first one by opening a browser in the virtual machine and trying to load any website. If that doesn’t work, you can usually solve the problem by rebooting the virtual machine or toggling the “enable networking” setting (turn off and then back on) from the dropdown menu near the top-right of your Ubuntu desktop. If that’s not the problem, I suggest that you move the Phamerator configuration file and allow Phamerator to recreate a default file: Steps to do this: Reboot the Virtual Machine Login as whichever account (seafaculty or seastudent) you prefer to use. (If you use both accounts, you will need to complete these steps logged in as each user.) Make sure Phamerator is NOT running. Open the terminal (click the Ubuntu “Dash” icon in the top-left corner, type “terminal” and hit the <enter> key) Paste in the following command: `mv ~/.phamerator/phamerator.conf ~/Desktop` Start Phamerator. You may need to update server to: http://phamerator.webfactional.com/databases_Hatfull and database to: Actino_Draft If prompted for a password, use: phage If everything appears to be in working order, you can delete the phamerator.conf file that is on your desktop. –Dan Edited 01 Mar, 2017 15:40

Link to this post | posted 01 Mar, 2017 15:39

DanRussell

Hi Nikki,

Did you try "phage" for the password? If phamerator ever wants a password, that's the one.

If that doesn't help, Steve recently answered a similar question via email, so I'm going to copy his response here:

It sounds like one of two things:
your virtual machine is unable to access the internet
your phamerator configuration file has become corrupted

You can test the first one by opening a browser in the virtual machine and trying to load any website. If that doesn’t work, you can usually solve the problem by rebooting the virtual machine or toggling the “enable networking” setting (turn off and then back on) from the dropdown menu near the top-right of your Ubuntu desktop.

If that’s not the problem, I suggest that you move the Phamerator configuration file and allow Phamerator to recreate a default file:

Steps to do this:
Reboot the Virtual Machine
Login as whichever account (seafaculty or seastudent) you prefer to use. (If you use both accounts, you will need to complete these steps logged in as each user.)
Make sure Phamerator is NOT running.
Open the terminal (click the Ubuntu “Dash” icon in the top-left corner, type “terminal” and hit the <enter> key)
Paste in the following command:
mv ~/.phamerator/phamerator.conf ~/Desktop
Start Phamerator. You may need to update server to: http://phamerator.webfactional.com/databases_Hatfull and database to: Actino_Draft
If prompted for a password, use: phage
If everything appears to be in working order, you can delete the phamerator.conf file that is on your desktop.

–Dan

Edited 01 Mar, 2017 15:40

Link to this post \| posted 02 Mar, 2017 20:21
c.sunnen	Thanks a bunch, Dan! Entering the "phage" password did the trick. As a side note, it appears that we may have encountered this problem by "force shutting down" Phamerator. Today, a student had this password request appear after re-starting Phamerator after it had been prematurely closed. Thanks again, Nikki

Link to this post \| posted 02 Mar, 2017 20:27
DanRussell	Hi Nikki, Glad it worked. Definitely shutting down the VM or closing your computer while Phamerator's running/doing things can cause problems. I'd always advise to close Phamerator before shutting anything else down. –Dan

Link to this post \| posted 23 Feb, 2019 13:24
deep	Hello All, I have made a PhamDB database of my genomes and now want to use phamerator but I do not see how to use phamerator? The standalone version is not supported anymore as I got to know. Thanks!

Link to this post \| posted 25 Feb, 2019 16:49
DanRussell	Deep kumar Hello All, I have made a PhamDB database of my genomes and now want to use phamerator but I do not see how to use phamerator? The standalone version is not supported anymore as I got to know. Thanks! Hi Deep, You need to contact Steve Cresawn (cresawsg@jmu.edu) and arrange to give him your database. He can make it available from the dropdown menu at phamerator.org. –Dan

Link to this post \| posted 25 Feb, 2019 19:26
deep	Dan Russell Deep kumar Hello All, I have made a PhamDB database of my genomes and now want to use phamerator but I do not see how to use phamerator? The standalone version is not supported anymore as I got to know. Thanks! Hi Deep, You need to contact Steve Cresawn (cresawsg@jmu.edu) and arrange to give him your database. He can make it available from the dropdown menu at phamerator.org. –Dan Thanks Dan - I will email him with my sql database I generated using PhamDB. So, phamerator is not longer available for standalone installation? And, please let me know if I want to align my assembled phage with the phage genomes I have in my database (that I will send to Cresaw), how can I do it in phamerator or any other medium? Because my assembled phage is not in genbank format. Thanks, DK

Link to this post | posted 25 Feb, 2019 19:26

deep

Dan Russell
Deep kumar
Hello All,

I have made a PhamDB database of my genomes and now want to use phamerator but I do not see how to use phamerator? The standalone version is not supported anymore as I got to know. Thanks!

Hi Deep,

You need to contact Steve Cresawn (cresawsg@jmu.edu) and arrange to give him your database. He can make it available from the dropdown menu at phamerator.org.

–Dan

Thanks Dan - I will email him with my sql database I generated using PhamDB. So, phamerator is not longer available for standalone installation?
And, please let me know if I want to align my assembled phage with the phage genomes I have in my database (that I will send to Cresaw), how can I do it in phamerator or any other medium? Because my assembled phage is not in genbank format.

Thanks,
DK

Link to this post \| posted 18 Apr, 2019 14:11
jlee04	A couple of my students can no longer log into Phamerator, getting error message: "Token expired" and are now forbidden from logging in. Thanks!

Link to this post \| posted 18 Apr, 2019 15:05
cdshaffer	I just tried online phamerator.org and was successful so it might have been a temporary issue. If it is still failing for the students I would suggest trying to create a new account as a work around, also posting to the chat on the phamerator page can't hurt.

Link to this post \| posted 18 Apr, 2019 18:22
scresawn	Hi Julia, are things working for you now?

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Locked out of Phamerator