Link to this post | posted 08 Feb, 2017 21:42

cdshaffer

Ok well it appears that flaverint does not crash my current "development" version of Starterator. So I can generate a whole phage report using it. The problem with the development version is that I have taken out much of the code that generates the summary text below the graph in anticipation of adding improved versions along the lines of the improvements to the single pham reports. Consequently the whole phage report that comes out has all the graphics but none of the summary text. So, no counting which starts are annotated and/or conserved and no list of base locations for the various starts in the phage being analyzed, this means the online version is still better for all that info. The good news is that these whole phage reports do have the part of the PDF that you need to upload to PECAAN and PECAAN will have the links to the online versions. Below are links to download the whole phage report for the crashing phage mentioned above as generated by the development version of starterator (for anyone interested the current development version is this branch of my person github repo). Whole phage pdf report for Aggie using development version of Starterator Whole phage pdf report for Flaverint using development version of Starterator Whole phage pdf report for Mattes using development version of Starterator Whole phage pdf report for Andies using development version of Starterator Whole phage pdf report for Philonius using development version of Starterator Whole phage pdf report for Aroostook using development version of Starterator Edited 08 Feb, 2017 22:21

Link to this post | posted 08 Feb, 2017 18:33

cdshaffer

OK looking into all these reports for phages aggie, philonious and Mattes, it appears these are phams that crash when you do a whole phage report but work when you ask for the individual phams. Very curious bug that will likely need time to solve. I would recommend that you use the pre-calculated web pages: for example pham 21476 results are available here: http://phages.wustl.edu/starterator/Pham21476Report.pdf Any other pham is available by just changing the pham number in the address above, so to get to pham 123 the URL would be: http://phages.wustl.edu/starterator/Pham123Report.pdf The issue I guess is PECAAN which requires a whole phage report, anyone using PECAAN let me know, I will work with you to find the best work around until I can find and fix the bug. Sorry but since this is not my own code it can be difficult for me to find bugs so I am not sure if it will be easy or difficult to solve this issue. Edited 08 Feb, 2017 21:22

Link to this post | posted 08 Feb, 2017 18:09
cdshaffer	Nick Pham 8250 does not crash when I use the SEA 2017 VM, so need a bit more background. Are you using the SEA 2017 VM or something else? Were you doing a single pham analysis of 8250 or a whole phage report on Flavrint and it crashed on gene 18?

Link to this post | posted 03 Feb, 2017 17:55

cdshaffer

If you are just creating a database that will not be updated then I would recommend just learning a bit of mysql. You might want to check out the mysql help sheet we created at the faculty retreat: https://docs.google.com/document/d/1SUUTojfDKwXCejGY1k14aY92hCqhe8XbDd_-qQPt_gQ/edit?usp=sharing and then just manually update the clusters using command like this: mysql> update phage set Cluster=”S” where Name=”Marvin”; just replace the bold parts with the cluster name and phage name in your database. If you think you will be constantly updating the phamerator database with phamdb I would focus on learning a bit of command line to run the update_clusters.py script (found in the plugins folder of phamerator) which needs a file with phage names and clusters. You can run the script each time after an update with phamdb.

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