Link to this post | posted 16 Sep, 2015 16:40

cdshaffer

We are using top agar with lividans and getting good plaques. Students are simply spreading phage solution on the plate, then adding top agar onto the plate with the spores already added to the top agar. Very Convenient, since it avoids the 15 min incubation step we did with phage + mycobacteria. Always nice in a class setting with limited time. So far so good for us, looks like we have at least a dozen phage isolated by direct plating. The hard part is growing and collecting the spores it adds time to prep work but they are expected to be stable throughout the phage isolation and purification stage so we only have to collect spores once. Edited 16 Sep, 2015 16:43

Link to this post | posted 11 Sep, 2015 20:45
cdshaffer	Dan, could you post the MD5 hash of the two images. I would like to confirm the integrity of the files after download. Thanks Chris

Link to this post | posted 23 Jul, 2015 20:44

cdshaffer

I tried TymAbreu_draft but that phage was not found, I have the most recent version of the Actino_draft database and in there the phage is no longer "_draft", its just Tymabreu. so I tested it out. Phage ran with no crashes, the likely culprit is confusion between the different "_draft" and current versions of the annotation. I suggest you use phamerator to update the actino_draft database and delete all the files in "Intermediate Files" folder (see the other "troubleshooting starterator" post) then try again. That is likely to work. However in case you need it, I posted the full phage report here. You can download from that link if the above suggestions fail to fix the problem on your system.

Link to this post | posted 19 Jul, 2015 21:05
cdshaffer	more info on phage dori crash the last two genes in dori are problematic, for both of these genes there are no in-frame stop codons upstream of the annotated start codon all the way to the end of the phage. This appears to be causing the crashes. I am slowly working on how best to modify code with minimal risk of breaking something else. Edited 22 Jul, 2015 16:43

Link to this post | posted 16 Jul, 2015 03:37
cdshaffer	phage Amela_Draft from the Actino_Draft database has also been reported to crash starterator.

Link to this post | posted 12 Jul, 2015 17:51

cdshaffer

OK I have that same error and stack trace for phage Dori pham 4536. Gene is the last gene and an orpham just ran snape got same crash, pham 26 of 100 ends up being pham 9858 and is also the last gene in the genome and is also an orpham. close inspection shows that this gene spans the ends and is annotated in DNA Master as going from 14 to 51601, however in phamerator the location is listed as just the part at the right end of the genome (i.e. 51601 to 52138 ). The predicted protein sequence is correct in phamerator database just not the right hand coordinate. This eventually leads to the crash. I can see in the code how this is handled for forward strand genes than span the end of the phage, but in these cases the coordinates are correct. Solution to handle this is non-trivial due to need to fix phamerator coordinates Edited 02 Aug, 2015 14:53

Link to this post | posted 08 Jul, 2015 21:53

cdshaffer

Yes I see that the current phamerator database now has nerujay and luchador out of draft stage. When I try on my local SEA 2015 image with same version of phamerator and database those phage work for me through the first 10 or so phams, so it looks like these issues might be local to your machine. From what I now understand about starterator I would suggest you try deleting all the old cache files in "/home/seastudent/.sterterator/Intermediate Files/". If that solves the issue we should probably add that to the instructions to try that first before posting about crashing phages. Edited 19 Jul, 2015 17:15

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