Link to this post | posted 19 Jan, 2022 01:04

cdherren

My version 5.32.6 build 2705, running as administrator, will update the database, but won't auto-annotate. It only says, "Annotation error". The log says it did everything, but there are no features and it opens an excel table with only headers and no data entries: Auto-annotation of Extracted from FastA Library Halo3.fasta begun at 6:59:44 PM Predicting genes at 6:59:44 PM Predicting tRNAs at 6:59:46 PM Parsing genes at 6:59:48 PM Learning genes at 6:59:48 PM Skipping BLAST at 6:59:49 PM Doing Profile at 6:59:49 PM Performing Frames Analysis at 6:59:50 PM Skipping Start Codon Analysis at 6:59:51 PM Performing Gray Holes Analysis at 6:59:51 PM Creating GC-Content Plot at 6:59:51 PM Auto-annotation Complete at 7:00:30 PM 2Kb

Link to this post | posted 19 Jan, 2022 01:22
debbie	Chris, I am guessing that you do not have all of the preferences set correctly. In particular, make sure that #2 and 6 are correct. Let me know, debbie

Link to this post | posted 20 Jan, 2022 18:39

cdherren

I got it to work. In the forums there is the older post for having 4 secure connections and then there's the DNA Master Update – Restores Genemark/Glimmer Functionality (9/14/17) that goes to 2 secure connections and changes the prediction settings. I merged the DNA Master Update – Restores Genemark/Glimmer Functionality (9/14/17) with the original DNA Master Installation Guide for a DNA Master Installation Guide (1.20.22) 179Kb

Link to this post | posted 20 Jan, 2022 19:17
cdherren	Are the best Gene Prediction addresses the FTP addresses in the online annotation guide or the opal.gatech and ncbi addresses?

Link to this post | posted 20 Jan, 2022 19:29
debbie	Chris, I am not sure what you are answering but do your DNA master preference panes look like this? Edited 20 Jan, 2022 19:40 637Kb

Link to this post | posted 20 Jan, 2022 21:38
cdherren	This is from the online manual 164Kb

Link to this post | posted 20 Jan, 2022 21:39
cdherren	This is from DNA Master Update – Restores Genemark/Glimmer Functionality (9/14/17) 207Kb

Link to this post | posted 20 Jan, 2022 21:51
debbie	Chris, We run Glimmer and Genemark on Pitt servers, so the update from 2017 is no longer applicable. debbie

Link to this post | posted 21 Jan, 2022 14:21
cdherren	So it's this one? 164Kb

Link to this post | posted 21 Jan, 2022 18:06
debbie	Yes. That matches the page I attached above. But don't get confused. It is not what appears in the Glimmer and GeneMark fields that is important. They could actually be empty. What is important is that the check box is checked and the the unlock code is entered.