Link to this post | posted 31 Oct, 2017 14:51
cdshaffer	Wait, there is a new list posted? I looked at seaphages.org under faculty info and phagesdb.org under workflow/annotations. Both those are the Nov 2015 version. Link please. Edited 31 Oct, 2017 14:53

Link to this post | posted 30 Oct, 2017 15:23

cdshaffer

I am not sure if this is the same issue since I did not see the exact error message but I had a student with a failed install. It turned out he had a high end "gaming" laptop which had two hard drives. A small fast SSD drive which was the "C:" drive, and a slower much larger "D:" drive. He chose to install on the D: drive and was never able to get DNA Master to work properly. It did work when he removed DNA Master and then ran an install on the C: drive. You might want to check with the student and see if he also had two hard drives and if so be sure to install on the C: drive.

Link to this post | posted 19 Oct, 2017 16:13
cdshaffer	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

Link to this post | posted 03 Oct, 2017 21:12

cdshaffer

As a follow up. I just tried running auto-annotation on DNA Master and got yet a different set of genes from what is on phagesdb. So my suggestion above will not actually help. I don't know where the discrepancies are coming from, but again likely from using different installations of glimmer/genemark to get the auto-annotation gene lists. The only way for you to get your DNA Master file in sync with the starterator/phagesdb would be to edit the DNA Master file by adding and deleting genes until the list matches up. We will have to wait and hear from Dan on why the phagesdb gene list does mot match the DNA Master auto-annotation.

Link to this post | posted 03 Oct, 2017 20:53

cdshaffer

I can confirm your results, when I run yeezus through the pecaan auto-annotation I get 86 gene prediction. Looking at the gene list on phagesdb I see 93 gene calls. Looking at it I can see for example that yeezus gene 7 called in phagesdb is missing from the pecaan auto-annotation. This difference in number of gene calls is likely due to minor differences in the settings used when running glimmer and genemark at the two different sites. When I run glimmer and genemark on my local machine I often get different results than what DNA Master got from the NCBI glimmer and genemark servers. Since the starterator results are based on the gene calls done by phagesdb, gene numbers will quite likely get out of sync with your DNAMaster file. Your best bet is to switch over to the new auto-annotation server inside DNA Master. There was an email with the instructions a couple of weeks back but here is a link to the pdf with instructions on how to get auto-annotation working in DNA Master. I believe once you set it up, you can just re-run auto-annotation in DNA Master and you should get the same 93 genes that are in phagesdb and starterator.

Link to this post | posted 27 Sep, 2017 18:44

cdshaffer

You can't really "merge" the two databases since mysql will just use pham numbers to decide whether to put proteins in the same pham. You want all similar proteins from both phage collections to be put in the same pham when they are similar to each other. The only way to do that is to rerun all the protein comparisons with all the proteins in the database. There is a thread on how to make databases using a web based program called phamDB. See this thread. The program is old enough now that the installation instructions are likely out of date and it will take some tweaking to install but the basic code is still sound. Alternatively, you could use K_phamerate scripts to create your database, you need to check out and use the code at the sea-phages github repository. That repository holds the code currently being used to create the phamerator databases and is being actively maintained by Travis Mavrich. Unfortunately you will have to install and run using command line.

Link to this post | posted 22 Sep, 2017 16:27

cdshaffer

Too bad none of the easy work arounds helped. I am going to assume that there are no important files inside the SEA VM, do NOT do the following if there are important files you need to recover from inside the VM. If you have files to recover you are going to need local expert who can work with your computer to get Ubuntu to boot so the files can be recovered, could be a long and arduous trial and error process of fixing Ubuntu. So assuming there are no files to recover, I would try to fix it by simply deleting and replacing the SEA VM. Sorry I don't use Virtualbox in Windows so some of this might be a little off but should suffice: 1. Open virtualBox program so you get something like this window (i think the pic is from mac, the windows version should look similar): 2. click on the "2017 SEA VM" in the left column and select "Remove…" from the machine menu 3. You should see a message about how you are "about to remove a machine from the machine list" and three buttons. Select "Delete all files" to completely remove and delete the SEA VM and all associated files 4. Go back to https://seaphages.org/software/virtualmachine/ and start with step two to reinstall the SEA VM, booting into Ubuntu and installing the guest additions.

Link to this post | posted 21 Sep, 2017 16:14
cdshaffer	Few things to try and report back: 1. Can you ignore the box, and just start phamerator? 2. What happens if you just click the red close button at the very top left? Does it still kick you back to the login screen? 3. Does this happen on both the student and faculty accounts? Edited 21 Sep, 2017 16:15

Link to this post | posted 22 Aug, 2017 16:29

cdshaffer

Sorry about that, we are having network upgrades here that have made it difficult to run the starterator updates. Until these are fixed starterator may lag a bit more than usual on when updates get posted. There was also a rollback of the phamerator database from version 141 back to version 140. I just rolled the starterator reports back so all the reports at phages.wustl.edu should now be in sync with version 140 which was run on 8/14/17 and should match phagesdb and phamerator.org.

Link to this post | posted 18 Aug, 2017 22:14

cdshaffer

just to document for anyone what wants to create an auto-annotation here is what I did: 1. open DNA Master and do the standard File -> Open Fasta and import the sequence 2. Go go https://discover.kbrinsgd.org/autoannotate/ and enter phage name and upload the same sequence file you used in step 1 3. Click "Process" 4. In the text box below the process button you will get the auto-annotation as "Documentation"; it will have a bunch of entries that look something like this: CDS 15 - 272 /gene="1" /product="gp1" /locus tag="Roots515_1" 5. Select and Copy the entire contents of that text box 6. Go back to DNA master, on the phage window click the "Documentation" tab at the top right 7. Delete any text in the large text box and paste in from the results from the PECAAN auto-annotation. (When I did this this step I got about 100 question marks at the end which I deleted so the last entry ended like this: CDS join(155929. .156288;1. .1 /gene="232" /product="gp232" /locus tag="Roots515_232" /note=Original Glimmer call @bp 155929 has strength 11.01 ** not called by GeneMark 8. click the parse button, then in the window that opens accept the defaults and click the new parse button. This will convert the "documentation" into DNA Master gene entries 9. Save the DNA Master file as usual Edited 18 Aug, 2017 22:22