SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 18 Feb, 2016 16:00
DanRussell	GregFrederick@letu.edu Dan Russell Hi Greg, The coding potential looks sparse on the reverse strand in that region. Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form? –Dan Dan: I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database. I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'. I did end up taking a quick look in Phamerator, and it seemed like the Final genomes all had removed that reverse-strand gene, while the Draft ones still had it. So probably dropping it is the way to go. –Dan

Link to this post | posted 18 Feb, 2016 16:00

GregFrederick@letu.edu
Dan Russell
Hi Greg,

The coding potential looks sparse on the reverse strand in that region.

Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form?

–Dan

Dan:

I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database.

I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'.

I did end up taking a quick look in Phamerator, and it seemed like the Final genomes all had removed that reverse-strand gene, while the Draft ones still had it. So probably dropping it is the way to go.

–Dan

Posted in: Gene or not a Gene → Cluster G genes spanning the COS site

Link to this post \| posted 16 Feb, 2016 21:12
DanRussell	coomansr All, We have the same. Do you suggest just using the other 2 databases or selecting another as a third? Roy Hi Roy, I think just going with the two recommended databases is fine. –Dan

Posted in: Functional Annotation → HHPred databases

Link to this post \| posted 12 Feb, 2016 22:16
DanRussell	Hi all, If you've successfully set up the SEA VM, but are still struggling with DNA Master, you might be interested in giving this new approach a shot. It allows you to run DNA Master within the SEA VM itself. It should be emphasized that this is a beta test only and is only recommended if you're an intrepid type and not worried about potential hiccups. That said, this has a lot of potential to be the future of how SEA-PHAGES uses DNA Master, and so any feedback we get would be welcome. I'll post a link to the instructions for doing this. Please use this forum to document any issues with the installation and/or running of DNA Master within the VM. http://seaphages.org/media/docs/DNA_Master_on_SEAVM_instructions.docx (Big thanks to Kristen Butela, Tammy Adair, Keith Hutchison, and others who have been troubleshooting non-Windows DNA Master.) Thanks, –Dan Edited 12 Feb, 2016 22:21

Link to this post | posted 12 Feb, 2016 22:16

DanRussell

Hi all,

If you've successfully set up the SEA VM, but are still struggling with DNA Master, you might be interested in giving this new approach a shot. It allows you to run DNA Master within the SEA VM itself. It should be emphasized that this is a beta test only and is only recommended if you're an intrepid type and not worried about potential hiccups. That said, this has a lot of potential to be the future of how SEA-PHAGES uses DNA Master, and so any feedback we get would be welcome.

I'll post a link to the instructions for doing this. Please use this forum to document any issues with the installation and/or running of DNA Master within the VM.

http://seaphages.org/media/docs/DNA_Master_on_SEAVM_instructions.docx

(Big thanks to Kristen Butela, Tammy Adair, Keith Hutchison, and others who have been troubleshooting non-Windows DNA Master.)

Thanks,
–Dan

Edited 12 Feb, 2016 22:21

Posted in: DNA Master → Beta Test: DNA Master within the SEA VM

Link to this post \| posted 12 Feb, 2016 15:08
DanRussell	Hi Greg, The coding potential looks sparse on the reverse strand in that region. Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form? –Dan

Posted in: Gene or not a Gene → Cluster G genes spanning the COS site

Link to this post \| posted 12 Feb, 2016 14:58
DanRussell	andersonr24@gator.uhd.edu Is it possible to be emailed the SeaVM file? I am a student and I am trying to annotate, but unable to comlplete without this file. Thanks! andersonr24@gator.uhd.edu Yep, just sent them to you. –Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 11 Feb, 2016 14:46
DanRussell	(Also, make sure you restart Phamerator once the database update is complete.)

Posted in: Phamerator → Seemingly "uneven" updating of Phamerator db

Link to this post \| posted 11 Feb, 2016 14:41
DanRussell	Hi Joe, The first—and most critical—thing to check is whether or not the students who don't have the newer phages are using the correct Phamerator database. To check the current database/server settings, go into one of their Phamerators and go to Edit –> Preferences. The current server and database should be: `server: http://phamerator.webfactional.com/databases_Hatfull` `database: Actino_Draft` If those are the settings, and you're still not seeing the recent phages, let us know. –Dan

Link to this post | posted 11 Feb, 2016 14:41

DanRussell

Hi Joe,

The first—and most critical—thing to check is whether or not the students who don't have the newer phages are using the correct Phamerator database. To check the current database/server settings, go into one of their Phamerators and go to Edit –> Preferences. The current server and database should be:

server: http://phamerator.webfactional.com/databases_Hatfull

database: Actino_Draft

If those are the settings, and you're still not seeing the recent phages, let us know.

–Dan

Posted in: Phamerator → Seemingly "uneven" updating of Phamerator db

Link to this post \| posted 11 Feb, 2016 14:27
DanRussell	Tamarah Adair Can someone please tell me how to share from the virtual box/phamerator files to the Mac desk top? Hi Tammy, Yes, setting up a shared folder as Chris described is perfect. (Just make sure you click "Auto-mount" as well, so it'll be loaded and ready to go each time you open the VM.) If you're using VirtualBox version 5.0 or later, you should be able to use Drag-and-Drop as well, though again as Chris mentioned it's still a bit buggy. To use this, open VirtualBox (not the VM itself yet) and select the VM just to highlight it. Click Settings–>General then click the "Advanced" tab. You should see a "Shared Clipboard" and a "Drag'n'Drop" setting. Put these both on "Bidirectional". Then launch the Virtual Machine and give it a shot. –Dan

Link to this post | posted 11 Feb, 2016 14:27

DanRussell

Tamarah Adair
Can someone please tell me how to share from the virtual box/phamerator files to the Mac desk top?

Hi Tammy,

Yes, setting up a shared folder as Chris described is perfect. (Just make sure you click "Auto-mount" as well, so it'll be loaded and ready to go each time you open the VM.)

If you're using VirtualBox version 5.0 or later, you should be able to use Drag-and-Drop as well, though again as Chris mentioned it's still a bit buggy. To use this, open VirtualBox (not the VM itself yet) and select the VM just to highlight it. Click Settings–>General then click the "Advanced" tab. You should see a "Shared Clipboard" and a "Drag'n'Drop" setting. Put these both on "Bidirectional". Then launch the Virtual Machine and give it a shot.

–Dan

Posted in: SEA-PHAGES Virtual Machine → Shared folders

Link to this post \| posted 11 Feb, 2016 14:17
DanRussell	cdshaffer …All my changes are freely available if anyone wants to download them and try their phage. You can get my version of the code from my github repository (github.com cdshaffer/starterator). Anyone comfortable with using the git command line to pull from a remote directory can easily download and test the code. My most recent branch is called filterSpanningGenes. Thanks again, Chris, for all this work. I think we should definitely formulate a plan to get an improved version of Starterator out to everyone. Perhaps it's something that could be part of the Faculty Retreat/Workshop this year and follow it up with some testing. It'd be great to even fix just some of the basic errors. –Dan

Link to this post | posted 11 Feb, 2016 14:17

DanRussell

cdshaffer
…All my changes are freely available if anyone wants to download them and try their phage. You can get my version of the code from my github repository (github.com cdshaffer/starterator). Anyone comfortable with using the git command line to pull from a remote directory can easily download and test the code. My most recent branch is called filterSpanningGenes.

Thanks again, Chris, for all this work. I think we should definitely formulate a plan to get an improved version of Starterator out to everyone. Perhaps it's something that could be part of the Faculty Retreat/Workshop this year and follow it up with some testing. It'd be great to even fix just some of the basic errors.

–Dan

Posted in: Starterator → Read First: Common Starterator Troubleshooting

Link to this post \| posted 09 Feb, 2016 20:48
DanRussell	Copying Fred's stuff from another thread to here, where it's best addressed. Thanks for all your help with this, Chris! Hopefully we can get some of these bugs permafixed soon. 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 20:48

DanRussell

Copying Fred's stuff from another thread to here, where it's best addressed. Thanks for all your help with this, Chris! Hopefully we can get some of these bugs permafixed soon.

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

Posted in: Starterator → phage that crash starterator

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