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Recent Activity
Glimmer Failure on Auto Annotation
| Link to this post | posted 15 Feb, 2016 20:48 | |
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Is anyone else having a problem with auto annotation today? It acts like it is working, but then gives a Glimmer failure and nothing is saved to Features. Auto-annotation of Extracted from FastA Library KylieMac.fasta9 begun at 2:46:10 PM Predicting genes at 2:46:10 PM Predicting tRNAs at 2:46:18 PM Parsing genes at 2:46:19 PM Learning genes at 2:46:19 PM Skipping BLAST at 2:46:19 PM Doing Profile at 2:46:19 PM Performing Frames Analysis at 2:46:19 PM Skipping Start Codon Analysis at 2:46:19 PM Performing Gray Holes Analysis at 2:46:20 PM Creating GC-Content Plot at 2:46:20 PM Auto-annotation Complete at 2:46:25 PM Profile for genome Extracted from FastA Library KylieMac.fasta9 Index,Name,Direction,Strand,Feature_Start,Feature_Stop,Feature_Length,Feature_Type, |
| Link to this post | posted 15 Feb, 2016 22:26 | |
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It is failing for me too. I can get to the web pages for glimmer and genemark directly on the web (the exact location can be found in DNA Master preferences; here is the link for glimmer) but when I try to run a glimmer or Genemark predictions on the web pages I get errors, here is an example: Job failed. Error Message : NCBI C++ Exception: Error: (CNetSrvConnException::eSrvListEmpty) "/netopt/ncbi_tools64/c++.by-date/production/20120616/GCC442-Release64/../src/connect/services/netservice_api.cpp", line 952: ncbi::CNetService::Iterate() — Couldn't find any available servers for the NS_Glimmer service. Submit new Data So it's a problem with NCBI, I posted a note to the help desk but mostly we are just going to have to wait until NCBI fixes the issue and of course it's the official dead presidents holiday so……. |
| Link to this post | posted 29 Mar, 2016 18:12 | |
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Was this problem ever resolved? I just tried running an auto-annotation and all I get back are tRNA calls and no protein-encoding genes. Lee |
| Link to this post | posted 31 Mar, 2016 00:28 | |
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Lee Hughes Well - seemed to be working fine today. Don't know what changed. Lee |
| Link to this post | posted 01 Apr, 2016 15:39 | |
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I had a similar problem that I got back only tRNA calls on Tuesday of this week. |
| Link to this post | posted 06 Sep, 2016 20:25 | |
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"Glimmer failure" for 2:18 students when we auto-annotated in class today. One is running Dna master on native OS and the other is using wine. Any suggestions? If not, I'm not sure what to do other than reinstall DNAmaster? Thanks in advance, -Emily |
| Link to this post | posted 13 Nov, 2016 06:53 | |
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Hi everyone, I am a student working with DNA Master and have had the same issue listed by several others on this forum. When I tried to annotate a genome from a fasta file, I got two error messages, "Glimmer Failure" and "Annotation Error" and have not been able to resolve either. I re-downloaded the fasta file, restarted the computer, restarted the program, and tried it with another genome that we have already successfully annotated and nothing seemed to work. Has anyone been able to find a solution? Thanks! |
| Link to this post | posted 15 Nov, 2016 21:11 | |
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NCBI has changed their website so that DNA Master cannot connect. You need to run the update DNA Master under the help menu and restart DNA Master to get to the newest version. Be sure to post if you have problems. |
| Link to this post | posted 16 Nov, 2016 15:08 | |
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Hi all, If you're experiencing recent problems with DNA Master, it's probably because of the update of NCBI to use secure connections. See the blog post and forum below, but the gist of it is that DNA Master was updated on Nov 15, 2016 to be able to handle this, so if you haven't updated your DNA Master since then, please do so! http://seaphages.org/blog/2016/11/16/dna-master-updated-use-secure-ncbi-connections/ http://seaphages.org/forums/topic/214/ –Dan |
| Link to this post | posted 13 Jan, 2017 03:58 | |
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It's back! I'm getting a Glimmer failure message. DNA Master has been updated to the 03 Dec 16 build. For both Sally and for me, a few days ago there was no problem. Today we both have problems. Actually, starting yesterday for her. Two thoughts/questions on the matter, that are not mutually exclusive. The first one is that it's now the beginning of the spring semester. What's the possibility we are choking the server with all the students coming online? The second one is how many of us who are having the problem are running DNA Master on a Mac using the wine configuration. DNA Master is clearly slow loading sequence information and I feel as if it is slower doing the BLASTing when run within wine. So maybe it is more sensitive to network speed or I/O rates in general? If so I'm compounding the problem working at home with a DSL connection. Just thoughts but it just seems the problems show up sporadically and random failures are sometimes an indication that one is pushing the margins of performance. Keith Dan Russell |