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

Link to this post | posted 27 Apr, 2016 16:52

cdshaffer

Wow! There were three genes in Kerberos that crashed starterator. These are all issues with protein names that is a known incompatability between Starterator and the phamerator database which needs work. Hopefully this will get addressed this summer. In the mean time I did get a starterator report of all the genes that did not crash (i.e. report is missing the three genes that crash but the rest are there.) I suggest for notes that you just put NA for the starterator comment for those three genes. You can download the complete pdf using this link. Edited 27 Apr, 2016 19:42

Link to this post | posted 19 Apr, 2016 14:05
cdshaffer	Good news, my run worked. Link to full report. Edited 19 Apr, 2016 15:01

Link to this post | posted 06 Apr, 2016 15:34

cdshaffer

Welcome to Unix! The problem is likely one of two issues. The most common is that you have a folder in the path with a space in the name. This can be any folder in the hierarchy starting with the very top all the way to the edit_dir. If you are using the SEA virtual machine this folder path will start like thie: /home/seastudent… and then proceed with each folder down to edit_dir. If you have any spaces in the names of any of those folders Consed will fail to find the files. This is why folder names so often have underscores (i.e. edit_dir not "edit dir". So check all your folder names. The second most common issue is that the entries in the .fof file are not exactly correct or were made with the wrong text encoding. Check the .fof file paying particular attention to case. Unix is case sensitive, so File.ab1 is not the same as file.ab1. Finally, if you made the .fof file in a text editor that uses either mac or dos encoding it can be unreadable by Consed. Consed requires unix encoding. Here is the protocol I use with my students: 1. create a new folder and put all the sequences files in that folder 2. cd to that folder in terminal 3. create the .fof file with the following command in terminal: ls *.ab1 > reads.fof 4. you will now see another file in the folder with the reads called "reads.fof" This reads.fof is unix encoded text file and is readable by Consed, also the computer is much better about avoiding typos. The user should open the reads.fof with a text editor and double check that the list of files looks good. Now proceed with step two in Dan's protocol and move the .ab1 files into the chromat_dir and the reads.fof file into the edit_dir. The above covers about 90% of the 512 errors, if neither helps you, post a followup.

Link to this post | posted 05 Apr, 2016 18:12
cdshaffer	OK, thanks for that phage, it revealed an error in my code for finding these end spanning genes. I finally got starterator to complete a run with more improvements to the code. You can get the report here. the end spanning gene is not in the report, you will just want to put NA for the starterator notes.