Link to this post | posted 03 Feb, 2017 17:21

cdshaffer

This was one of the issues that PhamDB did not implement as far as I know. The only way I know to add cluster info is manually (i.e. command line). You can either use a python script that is part of the phamerator distribution or just directly type in mysql commands to update the cluster. There are a lot of specific issues that will depend on your exact computer set-up so impossible to give exact commands. Are you using a SEA virtual machine?

Link to this post | posted 02 Feb, 2017 23:19

cdshaffer

I am curious, have you tried manually testing the NCBI glimmer page to see if it is working when you are getting the failures when trying to access with DNA Master? https://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi If that page is down then it is guaranteed DNA Master will fail. Also, have you tried increasing the time limit in the auto-annotation window? It defaults to 2 minutes, maybe if NCBI is slowing down responses setting DNA Master to wait longer would help.

Link to this post | posted 16 Jan, 2017 19:56

cdshaffer

I have checked on my mac, running DNA Master in a Windows 7 VM and the wine bottle version. Both worked for me so I can confirm that NCBI is up and running but it makes it difficult to diagnose why glimmer is failing for you. Just to check, I have version 5.23.1 from 03 Dec 2016, check yours, maybe the auto-update failed and you are still running an older version with the secure connections issue. As for the Key and access violations that should not be the cause of glimmer failure, see this page for more info and how to fix: http://phagesdb.org/DNAMaster/faq/

Link to this post | posted 16 Jan, 2017 17:53

cdshaffer

Katie, you have hit an issue I have been thinking about a lot lately as we change over to a distributed "all web" system. One of the things that phamerator does on occasion is move proteins to different pham numbers as it updates with new phages. It is pretty rare nowadays but it does happen. When this happens its possible for the various web pages to get "out of sync", each displaying info from a different version of the database. This general problem is a pernicious issue across the bioinformatics field so it is a really good teaching moment for your students. Long story short for you: Kevin1 gene 24 was in pham 21227 but it is now in pham 25384. You can see this if you go to phagesdb page for Kevin1 gene 24.

Link to this post | posted 10 Jan, 2017 02:34

cdshaffer

Curious, It is entirely possible there is a bug in the code that I added when going to v1.1 from the that beta version. I tested my most recent version and it did not crash on beardedlady. Unfortunately I am in the middle of updating the part of starterator that generates the pdf report. I got most of the issues with the single pham reports the way I want them but I have not updated the code to handle the "all phage" reports. I have posted the most recent version of a whole phage report here: phages.wustl.edu/BeardedLady_DraftReport.pdf but you can see there is still a lot I need to add back into the reports before they are useful again. It does have all the graphics tracks its just missing all the summary reports on annotated starts and all that. If you just use the graphical tracks the whole report should work, if you want all the text summary you will just have to stick with the beta version or go to phages.wustl.edu/starterator and get the pham report for each pham in the phage one by one.

Link to this post | posted 10 Jan, 2017 01:15

cdshaffer

Sorry I did get a chance to write some new code for starterator over thanksgiving in hopes of getting things into the VM but it was just not soon enough given the timing of the in silico workshop and the need to get the VM out to everyone attending. So if you are using the SEA 2017 and have not updated manually (using git command line), you still have the original version. You can still use the SEA 2017 VM but you will not get any of my updates. The current best way to get those reports is to use the pham reports I have been posting on the web. I post new reports every time there is a new phamerator database and I use my most recent code (for good or bad). To get those you can go here http://phages.wustl.edu/starterator to see a list of all the pham reports (for all phams with two or more members). Just scroll down till you find the link for the pham you are interested in and click the link. However given the length of the list, an easier technique is to just type in the address using the pham number since everything else in the address is identical. For example to get to the report for pham 21476 just type in this address http://phages.wustl.edu/starterator/Pham21476Report.pdf And if you want pham 66 just replace the 21476 in the above address with 66: http://phages.wustl.edu/starterator/Pham66Report.pdf

Link to this post | posted 10 Jan, 2017 01:07

cdshaffer

Sorry everyone but I had some free time to write code over thanksgiving in hopes of getting things into the VM but it was just not soon enough given the timing of the in silico workshop and the need to get the VM out to everyone attending. So if you are using the SEA 2017 and have not updated manually (using git command line), you still have the original version which does crash on quite a few phams. The current best way to get reports if the SEA 2017 VM crashes on your phage is to use the pham reports I have been posting on the web. I post new reports every time there is a new phamerator database and I use my most recent code so you might find them better than what you are getting from the VM. You can go here http://phages.wustl.edu/starterator to see a list of all the pham reports for all phams with two or more members, simply scroll down till you find the link for the pham you are interested in and click the link. However given the length of the list, an easier technique is to just type in the address using the pham number since everything else in the address is identical. For example to get to the report for pham 21476 just type in this address http://phages.wustl.edu/starterator/Pham21476Report.pdf

Link to this post | posted 02 Dec, 2016 23:08

cdshaffer

Everyone, I am happy to announce the release of version 1.1 of Starterator. This has several minor updates and bug fixes. It is available now from github.com/SEA-PHAGES/starterator. I have let Dan know and I expect he aleady has or will very soon the new SEA 2017 VM to this new version. I will be collaborating with Dan to create an update script which can be run to update the Starterator currently installed on a working VM. New features: 1. Better recognition of identical tracks which are then collapsed into a single track. Many phams now have significantly fewer tracks. 2. Tracks are now labeled with the name of the first phage on the list and indicate how many other phage are also represented in the track 3. Tracks now indicate the called start with a yellow bar if the start is Draft quality and a green bar if the start is based on published annotations 4. The report has been updated in several ways: A. The report now indicates the start which has been most often called in the published annotations and does not consider draft quality annotations when looking for the "most annotated" start. B. The "suggested starts" section has been depreciated as it was too often based on draft annotations which simply perpetuated the original Glimmer/Genemark calls. C. The run date has been added to the output so that changes in the phamerator database can be easily recognized and the most recent report used for analysis. 5. Many minor bugfixes We will post update info for those that wish to continue to use older VM's soon.

Link to this post | posted 02 Dec, 2016 22:33

cdshaffer

I would recommend that you update the VM this year as security updates for the old VM will be stopping sometime in 2017. This is why there is a new SEA VM. The new version uses Ubuntu 14.04 has updates through at least 2019. Web Phamerator will be available this spring but it is unknown how many features will make it into the final version. It can already make comparison maps and it is quite a bit faster so I will be using it in class ad the default. However, it is unclear how many of the advanced features will make it into the web version this year. For my class I have requested that VM be installed but I did that mostly for back-up (in case the network goes down) and access to advanced features (like access to the complete pham table).

Link to this post | posted 15 Nov, 2016 21:11
cdshaffer	NCBI has changed their website so that DNA Master cannot connect. You need to run the update DNA Master under the help menu and restart DNA Master to get to the newest version. Be sure to post if you have problems.