SEA-PHAGES | Auto-annotation fix for fall 2017 and later

Link to this post \| posted 21 Jan, 2022 20:05
cdherren	Got it!

Link to this post \| posted 08 Feb, 2022 00:26
amaya	debbie Chris, I am not sure what you are answering but do your DNA master preference panes look like this? Debbie, None of my students DNAMaster Preferences page looked like that -like the one on the manual and the one you have posted here. They were missing the bottom part (with the box checked) and the rest of the menu. They've installed DNAMaster from the link, and have updated and restarted, so I am not sure what else to do to get them to match the file from the guide. They also didn't have a Secure Connections tab (under Internet). One of them got the tRNAs autoannotated, but glimmer failure otherwise, and I think that that is related to these pages not being the same. I've sent them my auntoannotation for now and we are meeting again tomorrow so hopefully the y can do other functions of DNAMaster, but so far no autoannotations from them.

Link to this post | posted 08 Feb, 2022 00:26

amaya

debbie
Chris,
I am not sure what you are answering but do your DNA master preference panes look like this?

Debbie,
None of my students DNAMaster Preferences page looked like that -like the one on the manual and the one you have posted here. They were missing the bottom part (with the box checked) and the rest of the menu.

They've installed DNAMaster from the link, and have updated and restarted, so I am not sure what else to do to get them to match the file from the guide. They also didn't have a Secure Connections tab (under Internet). One of them got the tRNAs autoannotated, but glimmer failure otherwise, and I think that that is related to these pages not being the same. I've sent them my auntoannotation for now and we are meeting again tomorrow so hopefully the y can do other functions of DNAMaster, but so far no autoannotations from them.

Link to this post \| posted 08 Feb, 2022 15:53
DanRussell	amaya debbie Chris, I am not sure what you are answering but do your DNA master preference panes look like this? Debbie, None of my students DNAMaster Preferences page looked like that -like the one on the manual and the one you have posted here. They were missing the bottom part (with the box checked) and the rest of the menu. They've installed DNAMaster from the link, and have updated and restarted, so I am not sure what else to do to get them to match the file from the guide. They also didn't have a Secure Connections tab (under Internet). One of them got the tRNAs autoannotated, but glimmer failure otherwise, and I think that that is related to these pages not being the same. I've sent them my auntoannotation for now and we are meeting again tomorrow so hopefully the y can do other functions of DNAMaster, but so far no autoannotations from them. Hi Amaya, Are you sure they've updated DNA Master? What build number are they running? Because if they've successfully updated, they should have the Secure Connections tab. If they haven't, then we need to figure out what's preventing them from udpating. –Dan

Link to this post | posted 08 Feb, 2022 15:53

DanRussell

amaya
debbie
Chris,
I am not sure what you are answering but do your DNA master preference panes look like this?

Debbie,
None of my students DNAMaster Preferences page looked like that -like the one on the manual and the one you have posted here. They were missing the bottom part (with the box checked) and the rest of the menu.

They've installed DNAMaster from the link, and have updated and restarted, so I am not sure what else to do to get them to match the file from the guide. They also didn't have a Secure Connections tab (under Internet). One of them got the tRNAs autoannotated, but glimmer failure otherwise, and I think that that is related to these pages not being the same. I've sent them my auntoannotation for now and we are meeting again tomorrow so hopefully the y can do other functions of DNAMaster, but so far no autoannotations from them.

Hi Amaya,

Are you sure they've updated DNA Master? What build number are they running? Because if they've successfully updated, they should have the Secure Connections tab. If they haven't, then we need to figure out what's preventing them from udpating.

–Dan

Link to this post \| posted 08 Feb, 2022 16:10
debbie	Hi Amaya, We had this problem this summer. This fails because DNA master is set to an active FTP stie, and it has to be changed to passive. But until you get an update, you don't have that option. Kristen Butela was able to work through it, so try this. Be sure to be running as administrator as you update. From Kristen: I figured it out! For a fresh install, you need to first update DNA Master from the help menu. This appears to go through successfully, and I got the message about the update being finished after restarting the program. I then restarted the program, and this is where I was getting the error messages and eventual FTP failure when retrieving helper programs. However, I just ignored all of those messages and clicked to make them go away. After the "Retrieving Helper Programs" update finally stalled at the 3% mark and threw the ftp error message, I went back to Preferences. The Home Site button is now there, so that initial update round must have updated the Preferences panel. I just unchecked the Active FTP connection box and applied changes. I then re-updated DNA Master, and everything went through with no error messages. This is an easy work around that only takes a few extra seconds. I'm happy to make a video and post it to the forums if that would be helpful. Kristen

Link to this post | posted 08 Feb, 2022 16:10

debbie

Hi Amaya,
We had this problem this summer. This fails because DNA master is set to an active FTP stie, and it has to be changed to passive. But until you get an update, you don't have that option.
Kristen Butela was able to work through it, so try this. Be sure to be running as administrator as you update.
From Kristen:

I figured it out!

For a fresh install, you need to first update DNA Master from the help menu. This appears to go through successfully, and I got the message about the update being finished after restarting the program. I then restarted the program, and this is where I was getting the error messages and eventual FTP failure when retrieving helper programs.

However, I just ignored all of those messages and clicked to make them go away. After the "Retrieving Helper Programs" update finally stalled at the 3% mark and threw the ftp error message, I went back to Preferences. The Home Site button is now there, so that initial update round must have updated the Preferences panel. I just unchecked the Active FTP connection box and applied changes. I then re-updated DNA Master, and everything went through with no error messages. This is an easy work around that only takes a few extra seconds.

I'm happy to make a video and post it to the forums if that would be helpful.

Kristen

Link to this post \| posted 08 Feb, 2022 18:50
amaya.garciacostas	debbie Hi Amaya, We had this problem this summer. This fails because DNA master is set to an active FTP stie, and it has to be changed to passive. But until you get an update, you don't have that option. Kristen Butela was able to work through it, so try this. Be sure to be running as administrator as you update. From Kristen: I figured it out! For a fresh install, you need to first update DNA Master from the help menu. This appears to go through successfully, and I got the message about the update being finished after restarting the program. I then restarted the program, and this is where I was getting the error messages and eventual FTP failure when retrieving helper programs. However, I just ignored all of those messages and clicked to make them go away. After the "Retrieving Helper Programs" update finally stalled at the 3% mark and threw the ftp error message, I went back to Preferences. The Home Site button is now there, so that initial update round must have updated the Preferences panel. I just unchecked the Active FTP connection box and applied changes. I then re-updated DNA Master, and everything went through with no error messages. This is an easy work around that only takes a few extra seconds. I'm happy to make a video and post it to the forums if that would be helpful. Kristen Thank you!! I will project this post with the projector in class today!

Link to this post | posted 08 Feb, 2022 18:50

amaya.garciacostas

debbie
Hi Amaya,
We had this problem this summer. This fails because DNA master is set to an active FTP stie, and it has to be changed to passive. But until you get an update, you don't have that option.
Kristen Butela was able to work through it, so try this. Be sure to be running as administrator as you update.
From Kristen:

I figured it out!

For a fresh install, you need to first update DNA Master from the help menu. This appears to go through successfully, and I got the message about the update being finished after restarting the program. I then restarted the program, and this is where I was getting the error messages and eventual FTP failure when retrieving helper programs.

However, I just ignored all of those messages and clicked to make them go away. After the "Retrieving Helper Programs" update finally stalled at the 3% mark and threw the ftp error message, I went back to Preferences. The Home Site button is now there, so that initial update round must have updated the Preferences panel. I just unchecked the Active FTP connection box and applied changes. I then re-updated DNA Master, and everything went through with no error messages. This is an easy work around that only takes a few extra seconds.

I'm happy to make a video and post it to the forums if that would be helpful.

Kristen

Thank you!! I will project this post with the projector in class today!

Link to this post \| posted 12 Apr, 2022 02:05
akoga	Debbie, I am now having this problem with Auto-Annotation that so many others have described. I have checked my preferences several times and keep getting the error message that Glimmer failed, though, like others, I get Glimmer calls but not Genemark calls. My version says 5.23.6 Build 2705 Ann

Link to this post \| posted 12 Apr, 2022 02:28
debbie	Ann, I ran into this yesterday. Thee is nothing wrong on your end. we just need to reset the privilege. I'll make sure it gets done tomorrow. debbie

Link to this post \| posted 12 Apr, 2022 22:07
akoga	Thanks Debbie! It is working now! Ann

Link to this post \| posted 14 Mar, 2023 04:30
grosej	DNA master is not autoannotating for me in WINE, even after updating and changing to the correct server for glimmer and genemark. Ideas?

Link to this post \| posted 14 Mar, 2023 04:30
grosej	DNA master is not autoannotating for me in WINE, even after updating and changing to the correct server for glimmer and genemark. Ideas?

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Auto-annotation fix for fall 2017 and later