Link to this post | posted 08 Jul, 2015 21:33

cdshaffer

If starterator is crashing on your phage please try the possible solutions below. If these do not solve the problem then please post to the "phage that crash starterator" thread. It is important that we find the phage that crash starterator and this can only be done with your help. 1. Name of phage issues: I found that when I typed in phage name "Mana" it would crash but entering "Mana_draft" worked. The crashing in this case was due to some name confusion with Manad, probably because Mana is found entirely within Manad. So advice is to enter the phage name exactly as listed in Phamerator. 2. Some crashing issues have been fixed by deleting older files cached by starterator. These files can be found by going to your home directory, and select the menu item View -> "show hidden files" Once you select that, you will see many more files and folders in your home directory. Open the folder .starterator (note how the first character in the folder name is a period). Once inside that folder there is a folder called "Intermediate Files". I have fixed many crashes by deleting all files in that folder and running starterator again. 3. Some reports of crashing have been solved by increasing the memory available to the virtual machine. It is recommended that you give the machine 2048 MB. Larger phage may require more memory. To change the amount of memory used by the virtual machine you must shutdown the machine completely. Then select the machine in the left column and to go Settings -> System -> motherboard, use the slider to set the memory allocated to the virtual machine. Click OK and restart the machine. 4. Missing phages have been seen when using older virtual machines (i.e. 2014 & 2015 versions). This appears to be due to transition to the new "Actino_draft" database. You can check if this is the problem with your version of starterator. First check if the Actino_draft database is being used by phamerator by selecting Edit -> preferences in phamerator. Confirm that the database is called Actino_draft. If that is correctly set in phamerator see the next paragraph below on how to confirm that it is also set in starterator. If it is not set correctly in phamerator, go to the phamerator section of the forum by following this link. There you will find instructions for updating phamerator to the Actino_draft database. Do this update before you update Starterator. Assuming you have Actino_draft available in phamerator you can check if the same setting is also found in Starterator by using the similar Edit -> preferences menu. If you see Mycobacteriophage_Draft you should update that entry to Actino_draft as well. The other settings in Starterator preferences do not need to be changed. Edited 22 Jul, 2016 18:01

Link to this post | posted 05 Jul, 2015 17:45
cdshaffer	Phage Dori crashes starterator at pham 4563 mycobacteriophage_draft database see more info below on this crash Edited 19 Jul, 2015 17:14

Link to this post | posted 05 Jul, 2015 17:45
cdshaffer	Phage Redi crashes starterator at pham 3635, mycobacteriophage_draft database

Link to this post | posted 05 Jul, 2015 17:42
cdshaffer	Phage Mana crashes starterator. The exact pham where this occurs is unknown but I found the issue was a name confusion with phage Manad (probably because Mana in contained entirely within Mannad). I found that by entering the whole name as found in phamerator "Mana_draft" that the whole phage report was able to complete successfully.

Link to this post | posted 05 Jul, 2015 17:34

cdshaffer

This is a thread to collect the names of phage that crash Starterator. If you run across a phage that crashes phamerator, start by looking at the troubleshooting thread for things to try to get your things to work. If those tricks fail, please add your phage to the list below. For debugging purposes it would be very helpful to know the database and the specific pham that starterator was working on at the time of the error. The database is very likely "Mycobacteriophage_draft" unless it was specifically changed by the user. The exact value can be found by going to the starterator Edit -> Preferences menu and looking in the "Database Name" field. The pham can be seen in the Starterator status window which will be just behind the window with the crash message. See attachment for an example picture. Edited 12 Jul, 2015 20:12 21Kb