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PhamDB: Make your own Phamerator databases

| posted 19 Oct, 2017 02:10
Hi all!

I am trying to use the SEA PHAGES vm to view PhamDB databases and I am having a bit of trouble.
I follow the instructions for adding the server and database listed by PhamDB but then I get that "password required error". At that point I have to reinstall the machine to get rid of this error and to view the Actino_draft database once again.
After reaading some of Chris' comments else where I had a go at using the PhamDB address in the web browser in the VM and that can be reached, just not by Phamerator. On the same lap top outside of the VM, I am also able to contact the site.

Any thoughts about what could be going wrong?

All best,

Edited 19 Oct, 2017 02:27
| posted 19 Oct, 2017 16:05
Hi Heather,

As long as everything is precisely typed into Phamerator, I think this is likely to be a Phamerator-Ubuntu issue rather than a PhamDB issue. Check out the suggestions in this post and see if any of those might help. Sometimes, weird stuff can happen on the VM which sends Phamerator into strange cycles, but Steve had a couple suggestions.

| posted 19 Oct, 2017 16:13
If you are getting the "Database setup required" window that looks like this.

you just need to enter the root database password "phage" (without the quotes) to authorize updating the system. If you are getting a different kind of password error box can you send the exact wording or a pic.
Edited 19 Oct, 2017 16:18
| posted 19 Oct, 2017 19:26
Woooooo hoooooooo! Whooooooooo Hooooooo! WHAHAHAHAHAHHHHHHAAAAAAAAAH!

Thanks guys, that 'phage' password worked. I am in heaven.

| posted 20 May, 2020 12:43
hi,Dan, I have trouble with the creating database in the http://localhost, the create database button doesn't work, I cannot go to the next step, I have already uplouded the gb files, I donot know where is the problem, If you have any relevant solutions, please let me know, it will be my honor, looking forward to your reply, thanks a lot.
| posted 21 May, 2020 16:18
Database creation takes A LOT of computation and scales up exponentially with the number of phage.
Are you just working with 18 phage or did you add 18 phage to a larger database?
With 18 phage I would expect it to take at least a few minutes maybe up to 10, if you are adding phage to something larger it could take several hours to overnight. The last time I did this with ~100 phage on a pretty powerful computer it took over 2 hours.

The best way to get feedback and know if it is probably working is to use the utility in your OS that tells you how hard your CPU is working (either Activity Monitor on Mac or Task Manager in Win). If your phamdb is set up correctly, after you click the button you should see your CPU usage spike up and stay busy.
| posted 25 May, 2020 12:40
first, thank you for the respond, I had been tracked for sometime, and I just solove it by the vpn used, I could not knock into the button, not the time creating database. I've been learning some softwares recently in a locked area, I feel good because I finally figured it out, that was a question about the Internet, I thought I could open that interface and then it is no problem to create a database previously, I was wrong, the net was locked, that is the reason.

The 18 phages is just a test to a larger subsequent which would be founded by hundreds of phages.

Anyway, thank you very much for your reply. If there are any problems in the subsequent processing, I will continue to ask, I would really appreciate your continued help, thank you again. smilesmile
| posted 18 Jun, 2020 22:23
Hello, considering that I want to compare 2 o 3 phage genomes that are not on phamerator web, what it would be the best route to compare these genomes? I recently changed OS system from Windows to Ubuntu, but I did not find anything related to install or try phamerator in Ubuntu/Linux smile
| posted 19 Jun, 2020 17:47
I guess the answer depends on exactly what you are looking for in your comparison.

DNA master has a nice comparison tool if you only want to check a small number of genomes like you mention. Just like phamerator it will compare predicted protein sequences and group similar proteins into a single group that it assigns a unique color. The algorithm for comparison is not the exact same as phamerator so you get a "different but similar" kind of grouping but if all your phage are in the same subcluster it works pretty well. You will need DNA Master files of all the phage.

The DNA master protocol works really well for gene content analysis and moderately well if you are trying to see if you have called the same start sites as your comparison phage but for the later I have now switched to using the whole phage starterator report which I think is much better at doing a check of start codon choices. If you want a whole genome starterator please check out this thread:
It is trivially easy for me to set the run up and post the results, so always happy to run the analysis.
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