SEA-PHAGES | Read First: Common Starterator Troubleshooting

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 08 Jul, 2015 21:33

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 17 Aug, 2015 15:26
DanRussell	cdshaffer OK I thought it would be a good idea to have a thread with any solutions people have found for starterator crashing. I will start please feel free to add to the list. 1. Name of phage: 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. 2. Some crashes 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 and inside there is a folder called "Intermediate Files". I have fixed many crashes by deleting all files in that folder and running starterator again. Hey Chris, Thanks for documenting these issues. Hopefully, others can use these solutions, or we can eventually rework Starterator itself to avoid them! –Dan

Link to this post | posted 17 Aug, 2015 15:26

DanRussell

cdshaffer
OK I thought it would be a good idea to have a thread with any solutions people have found for starterator crashing. I will start please feel free to add to the list.

1. Name of phage: 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.

2. Some crashes 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 and inside there is a folder called "Intermediate Files". I have fixed many crashes by deleting all files in that folder and running starterator again.

Hey Chris,

Thanks for documenting these issues. Hopefully, others can use these solutions, or we can eventually rework Starterator itself to avoid them!

–Dan

Link to this post \| posted 19 Oct, 2015 16:23
cdshaffer	Dan, Is there anyway to make this post sticky so it stays on top of the list. Might be helpful to new faculty to read this post first and try solutions before posting a question. Could we even change the title to add something like READ THIS FIRST or START HERE. Chris

Link to this post \| posted 20 Oct, 2015 15:22
DanRussell	cdshaffer Dan, Is there anyway to make this post sticky so it stays on top of the list. Might be helpful to new faculty to read this post first and try solutions before posting a question. Could we even change the title to add something like READ THIS FIRST or START HERE. Chris Done and done. And just as an addendum, the currently posted versions of the 2016 SEA VM have the corrected default Starterator and Phamerator databases. If you download the new VMs now, each program should default to the Actino_Draft database. –Dan

Link to this post | posted 20 Oct, 2015 15:22

DanRussell

cdshaffer
Dan,
Is there anyway to make this post sticky so it stays on top of the list. Might be helpful to new faculty to read this post first and try solutions before posting a question. Could we even change the title to add something like READ THIS FIRST or START HERE.
Chris

Done and done. And just as an addendum, the currently posted versions of the 2016 SEA VM have the corrected default Starterator and Phamerator databases. If you download the new VMs now, each program should default to the Actino_Draft database.

–Dan

Link to this post \| posted 21 Oct, 2015 03:07
cdshaffer	Ok I tweeked the entry for missing phage.

Link to this post \| posted 02 Feb, 2016 17:08
fbaliraine	I have deleted all "Intermediate Files" folders in the cache as suggested by Dan Russell, "2. Some crashes 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 and inside there is a folder called "Intermediate Files". I have fixed many crashes by deleting all files in that folder and running starterator again." But "Andies_draft" still crashes at the same spot, stating "Startsaerator has encountered an error, please try again" as per attached snapshopt. Fred 28Kb

Link to this post | posted 02 Feb, 2016 17:08

fbaliraine

I have deleted all "Intermediate Files" folders in the cache as suggested by Dan Russell, "2. Some crashes 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 and inside there is a folder called "Intermediate Files". I have fixed many crashes by deleting all files in that folder and running starterator again."

But "Andies_draft" still crashes at the same spot, stating "Startsaerator has encountered an error, please try again" as per attached snapshopt.

Fred

Link to this post \| posted 09 Feb, 2016 17:47
ball.1766	I have tried all of the suggested fixes (checking the database, deleting intermediate files) but Starterator still crashes on Pham 11430 of WillSterrel_Draft every time I try to run it. Any suggestions would be appreciated since we start annotating it next week.

Link to this post \| posted 10 Feb, 2016 06:33
cdshaffer	Both Andies and Willsterrel appear to have issues that have already been solved as both ran fine on my copy with my bug fixes, links to full reports below: Full starterator report for Andies Full starterator report for WillSterrel

Link to this post \| posted 10 Feb, 2016 17:10
GregFrederick@letu.edu	cdshaffer Both Andies and Willsterrel appear to have issues that have already been solved as both ran fine on my copy with my bug fixes, links to full reports below: Full starterator report for Andies Full starterator report for WillSterrel That is awesome! Thanks Chris! Is your newest debugged version of Starterator available for distribution?

Link to this post \| posted 10 Feb, 2016 17:23
fbaliraine	Both Andies and Willsterrel appear to have issues that have already been solved as both ran fine on my copy with my bug fixes, links to full reports below. Thanks cdshaffer! Will appreciate receiving the bug-fixed:Starterator version.

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Read First: Common Starterator Troubleshooting