SEA-PHAGES | All posts created by NWCiowaSEAPHAGE

Link to this post \| posted 21 Sep, 2017 18:00
NWCiowaSEAPHAGE	1. Can you ignore the box, and just start phamerator? I don't think I can do that. I tried starting the virtual box and then the sea machine. I also tried starting the sea machine directly. When I start the sea machine directly I get the message in the attachment. 2. What happens if you just click the red close button at the very top left? Does it still kick you back to the login screen? Yup. It still kicks me out. 3. Does this happen on both the student and faculty accounts? Unfortunately yes. In the student account I can't even try to click any buttons. It kicks me back to the login screen almost immediately. 580Kb

Link to this post | posted 21 Sep, 2017 18:00

1. Can you ignore the box, and just start phamerator?

I don't think I can do that. I tried starting the virtual box and then the sea machine. I also tried starting the sea machine directly. When I start the sea machine directly I get the message in the attachment.

2. What happens if you just click the red close button at the very top left? Does it still kick you back to the login screen?

Yup. It still kicks me out.

3. Does this happen on both the student and faculty accounts?

Unfortunately yes. In the student account I can't even try to click any buttons. It kicks me back to the login screen almost immediately.

Posted in: SEA-PHAGES Virtual Machine → SEA-PHAGES Virtual Machine Error message

Link to this post \| posted 19 Sep, 2017 17:00
NWCiowaSEAPHAGE	I am getting an error message (different than the one posted in the forum last year - see attachment). If I click on either "report" or "cancel" it kicks me back to the screen that asks for a password. The error box moves a little within the upper left corner of my screen - almost blinking in and out. I've tried to reinstall the software and I've also updated the virtual machine. Neither made a difference. Any help someone can give me is most welcome! 1.39Mb

Link to this post | posted 19 Sep, 2017 17:00

NWCiowaSEAPHAGE

I am getting an error message (different than the one posted in the forum last year - see attachment). If I click on either "report" or "cancel" it kicks me back to the screen that asks for a password. The error box moves a little within the upper left corner of my screen - almost blinking in and out. I've tried to reinstall the software and I've also updated the virtual machine. Neither made a difference. Any help someone can give me is most welcome!

Posted in: SEA-PHAGES Virtual Machine → SEA-PHAGES Virtual Machine Error message

Link to this post \| posted 19 Aug, 2017 17:46
NWCiowaSEAPHAGE	I checked in this morning and my BLAST went just fine (and it was a large genome - over 150 kB). I'm not sure what to suggest. I'm no computer wiz. I kind of limp along and learn as I go. smg366 NWCiowaSEAPHAGE I got it to work this afternoon, actually! ! It's BLASTING as I type this Were you able to get BLAST to work? I have been trying to BLAST my genome in DNA Master for the past few days and it has not worked. I was wondering if this was specific to my computer or the program.

Link to this post | posted 19 Aug, 2017 17:46

NWCiowaSEAPHAGE

I checked in this morning and my BLAST went just fine (and it was a large genome - over 150 kB). I'm not sure what to suggest. I'm no computer wiz. I kind of limp along and learn as I go.

smg366
NWCiowaSEAPHAGE
I got it to work this afternoon, actually! ! It's BLASTING as I type this

Were you able to get BLAST to work? I have been trying to BLAST my genome in DNA Master for the past few days and it has not worked. I was wondering if this was specific to my computer or the program.

Posted in: DNA Master → Glimmer Failure on Auto Annotation

Link to this post \| posted 18 Aug, 2017 22:18
NWCiowaSEAPHAGE	I got it to work this afternoon, actually! ! It's BLASTING as I type this

Posted in: DNA Master → Glimmer Failure on Auto Annotation

Link to this post \| posted 04 Aug, 2017 15:45
NWCiowaSEAPHAGE	Hi Chris, I've got an account with PECAAN - thanks! I think I'll use some of it this semester. I've exported the GenBank file and saved it. When I open it in DNA Master it flickers up and then disappears…The first date I need the DNA Master file is August 24th so it's not truly urgent yet. However, I'm not sensing an easy solution is coming really soon so it you don't mind, I'd love to take you up on your offer to get a DNA master file for Roots515. Many thanks! I'm not sure how you will get that file to me but in case it is by email I'm at stolsma@nwciowa.edu. - Sara cdshaffer It is not you or your system. I am getting the same result. It looks like NCBI is no longer serving glimmer and genemark analysis as a web page (which is what DNA Master used) and is now forwarding all web requests for those pages to the download pages of the software. This totally breaks DNA Master auto-annotation as you have discovered. A long term solution is going to require updates to DNA Master. In the short term, it is probably easiest to use PECAAN. You can start here: https://seaphages.org/forums/topic/224/ Which explains how to get an account and a link to the user guide. PECAAN is under very active development so the user guide will help get you started but expect the actual web pages to be different. Pecaan is nice in that it will do a lot of the drudgery of entering notes in a proper format if you use it to do all your annotations. So you may want to consider switching over to using it for a lot of the annotation work. If you are in a huge hurry (like you need the DNA Master file ASAP for a class) just post the name of the phage I can use pecaan to generate the auto-annotation file for you very easily. If you want to try to use pecaan to do most of your annotation, feel free to post any follow=up questions to the PECAAN section of the forum.

Link to this post | posted 04 Aug, 2017 15:45

NWCiowaSEAPHAGE

Hi Chris,
I've got an account with PECAAN - thanks! I think I'll use some of it this semester. I've exported the GenBank file and saved it. When I open it in DNA Master it flickers up and then disappears…The first date I need the DNA Master file is August 24th so it's not truly urgent yet. However, I'm not sensing an easy solution is coming really soon so it you don't mind, I'd love to take you up on your offer to get a DNA master file for Roots515. Many thanks! I'm not sure how you will get that file to me but in case it is by email I'm at stolsma@nwciowa.edu.
- Sara

cdshaffer
It is not you or your system. I am getting the same result. It looks like NCBI is no longer serving glimmer and genemark analysis as a web page (which is what DNA Master used) and is now forwarding all web requests for those pages to the download pages of the software.
This totally breaks DNA Master auto-annotation as you have discovered. A long term solution is going to require updates to DNA Master.

In the short term, it is probably easiest to use PECAAN. You can start here:

https://seaphages.org/forums/topic/224/

Which explains how to get an account and a link to the user guide. PECAAN is under very active development so the user guide will help get you started but expect the actual web pages to be different. Pecaan is nice in that it will do a lot of the drudgery of entering notes in a proper format if you use it to do all your annotations. So you may want to consider switching over to using it for a lot of the annotation work.

If you are in a huge hurry (like you need the DNA Master file ASAP for a class) just post the name of the phage I can use pecaan to generate the auto-annotation file for you very easily.

If you want to try to use pecaan to do most of your annotation, feel free to post any follow=up questions to the PECAAN section of the forum.

Posted in: DNA Master → Glimmer Failure on Auto Annotation

Link to this post \| posted 02 Aug, 2017 02:57
NWCiowaSEAPHAGE	I'm still not getting auto-annotate to work. I updated DNA Master, shut everything down and restarted but continue to only get tRNAs to show up in my features tab after auto-annotating. I'm wondering if someone has figured out what the problem is and/or if you have any suggestions for me. Thanks!

Posted in: DNA Master → Glimmer Failure on Auto Annotation

Link to this post \| posted 19 Jul, 2017 02:50
NWCiowaSEAPHAGE	My DNA Master is updated. I checked the secure connections as suggested. I ran an auto-annotate last night and things went just fine. Tonight when I tried to auto-annotate a different phage genome all I got were tRNA genes. Any advice for me? Thanks! - Sara

Posted in: DNA Master → Glimmer Failure on Auto Annotation

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