Link to this post | posted 04 Aug, 2016 16:23

cdshaffer

Hmmm It's possible I didn't set things up correctly so I we need to "divide and conquer". The first step is a good network connection, it could be that the VM cannot get to the internet to download. Can you see if your VM can connect to the internet? You can check that easily by opening a browser and seeing if you can load seaphages.org from inside the SEA virtual machine. If that works then your network is up and running so start up Starterator again and see if the update to v1.1.1 works. I know my VM often loses network connection (I am using VirtualBox), for me a simple reboot of the VM usually fixes the network, if you have confirmed that the network is up and running and the update still fails, post another message here and we can proceed to the next step. Edited 04 Aug, 2016 16:25

Link to this post | posted 04 Aug, 2016 03:58

cdshaffer

A new beta version of Starterator has been posted. If you are running the current Beta version you should recieve an automatic update the next time you start up Starterator. If the update succeeds you will see the new version 1.1.1 in the title of the Starterator window. If you are not running the beta version and would like to install it, see the beta release post in this Starterator forum. This version has several updates and improvements: 1. New updated protocol for grouping genes into a single track. Some visually identical genes that were not being properly grouped. 2. Changes to individual track graphics: a. Change number of labels from 5 to 1 b. Annotation starts differ by color: yellow are auto-annotations (i.e. draft quality); green are starts published in GenBank 3. Change error message to recommend checking the Starterator Troubleshooting guide in seaphages forum when getting crashes 4. Whole genome analysis now creates a text file for PECAAN so you don't need to copy/paste out of the PDF. I have done limited testing on this but it appears to work (feedback appreciated if it does not work for you). You will find the text file in the "Intermediate Files" directory found inside the .starterator folder (see item 2 of the troubleshooting post in this forum if you don't know how to get to that folder), the file name will start with the name of the phage and end with "SuggestedStarts.txt". 5. Many minor bug fixes Thanks to everyone for all the beta testing and feedback, please do continue to get in touch with any and all problems or ideas for improvements.

Link to this post | posted 30 Jul, 2016 03:42
cdshaffer	Ok tried jabith once and it worked all the way through so I posted the results here. That was with the original version. As with Sprinklers I will try with the beta version see if I can get it to crash there. I will let you know how those go, please if you have time try the solutions suggested above as well and let me know if those stop the crashing.

Link to this post | posted 30 Jul, 2016 03:38

cdshaffer

OK, I tested Sprinklers on the original version of Starterator and it did not crash. You can download that report from this link. I tested it on Beta version next and it did not crash the first time but when I tried again it did crash. You can download the output from the first run of the beta version with the yellow and green starts from this link. These intermittent problems are very difficult to track down. Can you try the troublshooting solutions given in the first post of the "Read First: Common Starterator Troubleshooting" thread and report back it any of those helped. I wonder if it the problem with either the memory (which can easily change from run to run) or maybe the "Intermediate Files" issue.

Link to this post | posted 29 Jul, 2016 19:40

cdshaffer

Just back from meetings. I am testing phage Sprinklers now, will test phage jabith after that. If the beta version is failing on everything can you try two things and post the results: 1. Delete all the files in the "Intermediate Files" folder and try the beta version again. How to delete these files is explained in the thread "Read First: Common Starterator Troubleshooting" as item 2 of the first post. I have been having difficulty lately that is solved if I delete all those files. 2. Login to the student account and try the original version of Starterator and post whether things are crashing there or not, this will help isolate problems with the beta version from problems with Starterator in general. If you installed the beta version in the student account just post that you don't have access to the original version anymore. I will also remind any readers that it is a good policy to periodically delete all those files in the "Intermediate Files" folder. Edited 29 Jul, 2016 19:40

Link to this post | posted 26 Jul, 2016 17:37

cdshaffer

I have been playing with the graphical output for the gene tracks with the idea of indicating conservation. I have found that it would be very difficult to change the property of the line that indicates the chosen start site but I can easily manipulate the start labels. I have tried several changes that can be mixed and matched: 1. Change color of start label if that start is "highly conserved" 2. Set the labels to be dark or faint based on level of conservation (for example less conserved starts have a light grey label, strongly conserved starts have a dark black label) 3. Change the number of times that the track label appears on the track I have posted two examples with several phams in each. Example 1 increase font size of labels, change color to red if start is "highly conserved" (>95%), set grey level of label from 25% to 100% based on level of conservation. https://wustl.box.com/s/oq7fq654et6v27vyl2qqn6fhq4ode7yd Example 2 increase font size of labels, change color to red if start is "highly conserved", other labels are faint blue to dark blue based on level of conservation, set number of track labels to 1. https://wustl.box.com/s/9rmx88699z9mz34miy9beyyqvvasreom Comments/feedback appreciated

Link to this post | posted 21 Jul, 2016 21:58

cdshaffer

I would appreciate any and all suggestions for how to improve starterator graphics output. The latest version has green and yellow indicators on each track for annotation starts instead of the older blue. These marks were updated to indicate annotated starts based on thier provenance. The green annotated starts are based on non-draft status entries in the phamerator database (i.e. based on submitted annotations which have been reviewed). The yellow annotated starts are based on the start called in the "draft" annotations (i.e. based on Glimmer/GeneMark only). Are there other updates that you can think of that would make for a better experience? or things that your students found confusing that could use clarification? Please post your ideas below. For example in the July 20th SMART meeting Lee asked for an indication of the level of conservation of each start. I am looking into this and will post updates here. Other ideas: Is there any other information you would find informative on the first few pages or at the end or each pham? Any input is useful.

Link to this post | posted 21 Jul, 2016 21:02

cdshaffer

If you install your beta version into the SEA Faculty account you should see an icon for starterator on the Desktop. You will need to double click this icon. To double check that you are running the right version you will see the version in the title of the main starterator window if you have the beta or alpha version. In the image the title bar has the version "v1.1.0-beta" If you do not see the version title you expect please post issues to this forum.

Link to this post | posted 19 Jul, 2016 14:24

cdshaffer

Installation of Starterator Beta version Updates to Starterator are now available. This is currently a beta version that needs further testing prior to general release. The beta version has updates which have solved some of the issues which cause starterator to crash. Please post any problems with installation or subsequent use of the beta or alpha versions of this software to this discussion. Also, if you find new phages that crash this version of starterator, please try the solutions suggested under the topic "Read First: Common Starterator Troubleshooting" of this forum. If those fail to solve the problem, please report the name of the phage under the topic "phage that crash starterator". It is only through reports like these that bugs can be found and squashed. This beta version has many bugfixes and improved graphics. However, to be safe it is recommended that you install the program in the SEAFaculty account. This will keep the original release version available in the SEAStudent account as a back-up should the beta version fail. Here are the instructions for installing and using the beta version of Starterator. Once installed there should be an icon on the Desktop to run Starterator. The basic instructions for installation of the beta version are nearly identical to installation of the initial release version of Starterator. Download and follow the instructions with the following exceptions: http://phagesdb.org/media/docs/Starterator_installation_2015.pdf Change step 1 from: 1. Download the script installStarterator.sh from: http://phamerator.webfactional.com/installStarterator.sh to: 1. Download the script installBetaStarterator.sh from: https://wustl.box.com/v/installBetaStarterator Change step 5 from: 5. After navigating to this folder, run the script by typing, in Terminal: bash installStarterator.sh to: 5. After navigating to this folder, run the script by typing, in Terminal: bash installBetaStarterator.sh If you want to have even more updates you can install the alpha version. The instructions are the same except you should download and run installAlphaStarterator.sh instead. It can be found here: https://wustl.box.com/v/installAlphaStarterator

Link to this post | posted 16 May, 2016 15:18

cdshaffer

in phamerator select "Phages" in left column, then select the phage you want. Then in the magic appearing menu at the top select File -> Export Proteins (fasta) save the file, it is a text based multi-fasta file which you can open with any text editor to view and load into GEPARD for dotplot. You can also get all proteins sequences for any phage in GenBank: go to genbank record (easy from phagesdb phage page), in upper right corner click "Send", then select Coding sequences, then pick if you want the sequences as nucleotide or amino acids. The downloaded file will also contain all the gene sequences as a text file. Very similar to the file from phamerator but with a lot more info in the header line for each gene which can either be useful if you need any of that info or just in the way if you don't