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

Link to this post \| posted 20 Feb, 2018 22:32
GregFrederick@letu.edu	I just figured out what was going on with only auto-annotating the tRNA genes. I was working on a computer lab computer which I had set preferences on previously. But apparently DNA Master over-rode those preferences on an update at some point. Something reset the preferences to the default "Use NCBI servers". Anyway, once I went through again and reset the server settings as listed in the page below everything worked again. https://seaphages.org/media/docs/DNA_Master_Gene_Prediction_Settings.docx I hope this helps save headaches for someone else. Greg

Link to this post | posted 20 Feb, 2018 22:32

I just figured out what was going on with only auto-annotating the tRNA genes.

I was working on a computer lab computer which I had set preferences on previously. But apparently DNA Master over-rode those preferences on an update at some point. Something reset the preferences to the default "Use NCBI servers".

Anyway, once I went through again and reset the server settings as listed in the page below everything worked again.

https://seaphages.org/media/docs/DNA_Master_Gene_Prediction_Settings.docx

I hope this helps save headaches for someone else. Greg

Link to this post \| posted 11 Feb, 2019 02:26
d.zambito	Hello, I'm having a strange problem with the auto annotation in DNA Master. I am running the latest update of DNA Master (5.23.3; 08Jan2019), and all the preferences are updates as per the 2017 fix. When auto annotating, I get a "Glimmer failure", but interestingly, I do get auto annotated features. The start sites are all predicted by Glimmer, but no features have start sites predicted by GeneMark. I am connected to the internet and can BLAST individual genes without a problem. I have tried several times to autoannotate today without any luck getting the GeneMark predicted starts. Any suggestions? Thanks, Dana Pape-Zambito

Link to this post | posted 11 Feb, 2019 02:26

d.zambito

Hello,
I'm having a strange problem with the auto annotation in DNA Master. I am running the latest update of DNA Master (5.23.3; 08Jan2019), and all the preferences are updates as per the 2017 fix.
When auto annotating, I get a "Glimmer failure", but interestingly, I do get auto annotated features. The start sites are all predicted by Glimmer, but no features have start sites predicted by GeneMark. I am connected to the internet and can BLAST individual genes without a problem. I have tried several times to autoannotate today without any luck getting the GeneMark predicted starts.
Any suggestions?

Thanks,
Dana Pape-Zambito

Link to this post \| posted 11 Feb, 2019 11:20
debbie	Dana, Hi. I believe that the issue is a licensing issue that we need to do on our end. It should be fixed later today. debbie

Link to this post \| posted 11 Feb, 2019 22:12
debbie	I believe that GeneMark is now working! Back in business! debbie

Link to this post \| posted 11 Feb, 2019 22:12
d.zambito	Thanks Debbie. I was able to auto annotate this afternoon with GeneMark calls. -Dana

Link to this post \| posted 03 Dec, 2019 16:07
m.kanther	I am having this same problem today! d.zambito Hello, I'm having a strange problem with the auto annotation in DNA Master. I am running the latest update of DNA Master (5.23.3; 08Jan2019), and all the preferences are updates as per the 2017 fix. When auto annotating, I get a "Glimmer failure", but interestingly, I do get auto annotated features. The start sites are all predicted by Glimmer, but no features have start sites predicted by GeneMark. I am connected to the internet and can BLAST individual genes without a problem. I have tried several times to autoannotate today without any luck getting the GeneMark predicted starts. Any suggestions? Thanks, Dana Pape-Zambito

Link to this post | posted 03 Dec, 2019 16:07

m.kanther

I am having this same problem today!

d.zambito
Hello,
I'm having a strange problem with the auto annotation in DNA Master. I am running the latest update of DNA Master (5.23.3; 08Jan2019), and all the preferences are updates as per the 2017 fix.
When auto annotating, I get a "Glimmer failure", but interestingly, I do get auto annotated features. The start sites are all predicted by Glimmer, but no features have start sites predicted by GeneMark. I am connected to the internet and can BLAST individual genes without a problem. I have tried several times to autoannotate today without any luck getting the GeneMark predicted starts.
Any suggestions?

Thanks,
Dana Pape-Zambito

Link to this post \| posted 03 Dec, 2019 17:52
debbie	Dana, Thanks for the heads-up. This periodically happens due to the way GeneMark makes this available. It is corrected. Your auto-annotation should now include Glimmer and GeneMark calls. debbie

Link to this post \| posted 14 Dec, 2019 02:20
smg366	I am using DNA Master Version 5.23.2 from 11 Dec 2017. For the past few weeks, when a run the auto-annotation I get a blank features table. Today I decided to export the information from PECAAN to populate the table. This worked, but when I close the file and try to reopen it I get a "range check error". I have tried on multiple computers, but can't get the auto-annotation to work. When I try to run the update, that also doesn't work. The update runs, but there is no window saying I should close DNA Master. When I eventually try to close it, it has not updated. Any help would be much appreciated. Thanks, Susan

Link to this post | posted 14 Dec, 2019 02:20

smg366

I am using DNA Master Version 5.23.2 from 11 Dec 2017. For the past few weeks, when a run the auto-annotation I get a blank features table. Today I decided to export the information from PECAAN to populate the table. This worked, but when I close the file and try to reopen it I get a "range check error".

I have tried on multiple computers, but can't get the auto-annotation to work.

When I try to run the update, that also doesn't work. The update runs, but there is no window saying I should close DNA Master. When I eventually try to close it, it has not updated.

Any help would be much appreciated.

Thanks,
Susan

Link to this post \| posted 14 Dec, 2019 12:57
debbie	Susan, Hi! Start by updating your DNA Master. The current version is 5.23.3 Build 2639 from November 6, 2019. So the exact dates escape me, but the reason (I think) your version may not be working is that you do not have DNA Master pointing to the right servers. We have Glimmer and GeneMark running on our own servers. Go to 'Setting your Preferences' in the Bioinformatics Guide to check. If you still are having problems, there are more options. debbie

Link to this post | posted 14 Dec, 2019 12:57

debbie

Susan,
Hi! Start by updating your DNA Master. The current version is 5.23.3 Build 2639 from November 6, 2019.
So the exact dates escape me, but the reason (I think) your version may not be working is that you do not have DNA Master pointing to the right servers. We have Glimmer and GeneMark running on our own servers. Go to 'Setting your Preferences' in the Bioinformatics Guide to check.
If you still are having problems, there are more options.
debbie

Link to this post \| posted 20 Jan, 2020 22:55
nancyguild	Dear Dan, I am only getting tRNAs annotated on DNA master. When I go to preferences and click on internet I do not have the option of entering a password for the pbi server. Instead the NCBI glimmer and genemark sites are listed. I have attached a screen shot of what I am seeing . Any suggestions? Thanks, Nancy 77Kb

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Auto-annotation fix for fall 2017 and later