Link to this post | posted 28 Jan, 2017 18:44

kwhutch

I'm back to the opinion that perhaps collectively as a community or perhaps just with in our classes having students submitting within a limited time window maybe be choking the Glimmer server. I do know the NCBI, at least in the past, slows down response to BLAST calls when coming in from the same IP domains. Anyhow, I've seen the Glimmer error myself and with students running the Wine-Mac version and I've seen it with students running Windows 10 and I've seen it with Linux machines running DNA Master through Wine. However, I've also seen that without changing a thing but doing a repeated submission it eventually goes through. I had a student do this during class on Wednesday and Glimmer finally responded. All that said, we decided this year to let the students try it, but it wasn't worth their time and frustration to re-confirm Einstein's definition of insanity. So I auto-annotated and BLASTed the genome sequences we'd received and made available the dnam5 files after having them try for a couple days. It's one thing if they've not taken the time to set up DNA Master correctly. Another if everything is set up correctly and the problem is something out of their hands or ours. Edited 28 Jan, 2017 18:46

Link to this post | posted 30 Jan, 2017 13:58

mxo11

Keith and all, I agree. I've tried all possible permutations (from installing and reinstalling, changing privileges, adjusting compatibility to different Win versions… even running auto-annotation at ungodly hours) and the problem persists. My students all run DNA Master on desktops running Win 7 without any trouble (except when trying web tools -> Blast: the page can't be opened); I'm the only one running it on a Win10 VM. So, for the time being, in order to keep up with what my students are doing, I'll run the auto-annotation and BLASTing on a loaner laptop running Win7 (I also want to be able to do this with my students at the same time). Cheers, Manuel Edited 30 Jan, 2017 14:02

Link to this post | posted 01 Feb, 2017 17:56
mxo11	So, I updated DNA Master to the latest version (the build released a couple of days ago, on 29 January). Still, can't auto-annotate because of GLIMMER failure! Has any one seen this? Has anyone installed DNA Master on a Win10 VM? Does it work?

Link to this post | posted 02 Feb, 2017 22:21

kbutela

I'm running WINE DNA Master (29 Jan 2017 update) on a Mac OSX El Capitan 10.11.6, XQuartz version 2.7.6. I just ran autoannotation on some test files, and Glimmer appears to be working. Occasionally, I have encountered the Glimmer failure error, and just redoing the autoannotation later seemed to fix the problem. Keith's suggestion that the Glimmer servers may be getting clogged or rejecting multiple queries from the same IP domain in a limited amount of time may be a good explanation of what's going on.

Link to this post | posted 02 Feb, 2017 23:19

cdshaffer

I am curious, have you tried manually testing the NCBI glimmer page to see if it is working when you are getting the failures when trying to access with DNA Master? https://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi If that page is down then it is guaranteed DNA Master will fail. Also, have you tried increasing the time limit in the auto-annotation window? It defaults to 2 minutes, maybe if NCBI is slowing down responses setting DNA Master to wait longer would help.

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

Link to this post | posted 19 Jul, 2017 17:12

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 19 Jul, 2017 21:16
debbie	When you cannot connect to the DNA Master server, you will get a false message that says you have the latest version of DNA Master. An error message of Glimmer failure is a strong indication that you do not have the DNA master update. I will have a work around tomorrow.

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!

Link to this post | posted 02 Aug, 2017 14:51
debbie	There are multiple issues going on right now with servers. Chris Shaffer is right. The short answer for now is to auto-annotate in PECAAN and open the GenBank file it creates in DNA Master. (See Chris's message above.)