Link to this post | posted 03 Oct, 2017 20:53

cdshaffer

I can confirm your results, when I run yeezus through the pecaan auto-annotation I get 86 gene prediction. Looking at the gene list on phagesdb I see 93 gene calls. Looking at it I can see for example that yeezus gene 7 called in phagesdb is missing from the pecaan auto-annotation. This difference in number of gene calls is likely due to minor differences in the settings used when running glimmer and genemark at the two different sites. When I run glimmer and genemark on my local machine I often get different results than what DNA Master got from the NCBI glimmer and genemark servers. Since the starterator results are based on the gene calls done by phagesdb, gene numbers will quite likely get out of sync with your DNAMaster file. Your best bet is to switch over to the new auto-annotation server inside DNA Master. There was an email with the instructions a couple of weeks back but here is a link to the pdf with instructions on how to get auto-annotation working in DNA Master. I believe once you set it up, you can just re-run auto-annotation in DNA Master and you should get the same 93 genes that are in phagesdb and starterator.

Link to this post | posted 03 Oct, 2017 21:12

cdshaffer

As a follow up. I just tried running auto-annotation on DNA Master and got yet a different set of genes from what is on phagesdb. So my suggestion above will not actually help. I don't know where the discrepancies are coming from, but again likely from using different installations of glimmer/genemark to get the auto-annotation gene lists. The only way for you to get your DNA Master file in sync with the starterator/phagesdb would be to edit the DNA Master file by adding and deleting genes until the list matches up. We will have to wait and hear from Dan on why the phagesdb gene list does mot match the DNA Master auto-annotation.

Link to this post | posted 10 Oct, 2017 13:34
ashley2	Thanks, Chris. Ashley and Tammy Adair Edited 10 Oct, 2017 13:35

Link to this post | posted 10 Oct, 2017 14:08
debbie	I asked the folks who are running the auto-annotations to check their settings. They have confirmed that they are using the same settings/versions. It is my understanding that Glimmer and GeneMark use a random 'sample' of the genome and to the best of my knowledge that explains the discrepancies. That explains why hand curation and the work we do with these genomes is so necessary.

Link to this post | posted 17 Oct, 2017 19:18
tdelia	I have updated DNA Master for secure connections, and have updated to use the PBI server and I still get only tRNAs returned for auto-annotation. Is this still a problem or maybe I have settings wrong? I have tried several times on several computers. Thanks for any advice.

Link to this post | posted 17 Oct, 2017 20:22
debbie	Tom, Hi. Not sure if I can help, but let's see. What build of DNA Master are you running? It should be Build 2529. What fasta file are you using? If it will help, you can call me. debbie

Link to this post | posted 08 Sep, 2020 19:17
JChahal	Hey! 4 of my students had "Glimmer failure" pop up when trying to auto-annotate. They have the updated version of DNA Master. Some students were able to auto-annotate so I'm not sure what the issue is? Best, Jasmin

Link to this post | posted 08 Sep, 2020 19:52

debbie

Jasmin, HI. There are 2 common errors that can cause this. One is that our permission to use the Glimmer server ran out and needs to be updated. I have ruled that out because I was able to auto-annotate and obtain Glimmer results. The second reason is usually that the settings are incorrect in Preferences. Have them check # 2 at this page of the guide. The unlock code is Hatfull; there is no password. https://seaphagesbioinformatics.helpdocsonline.com/article-66