Link to this post | posted 24 Sep, 2020 12:02
scaruso	Thank you. I am going to advise they use Aragorn for now and revisit with tRNAScan-SE later in the semester, unless you suggest otherwise. Steve

Link to this post | posted 24 Sep, 2020 10:22
scaruso	Hello, Several students have reported to me that they are not getting results from tRNAScan-SE over the last week. So I just tried it, and let it run all night and had the same experience. It just stalled while working on a cluster BE, which has lots, and lots of tRNAs. Does anyone know something about tRNAScan-SE? Thanks, Steve

Link to this post | posted 09 Sep, 2020 01:47
scaruso	I need a way to more easily see their screens. Steve

Link to this post | posted 09 Sep, 2020 01:47
scaruso	Darn it. I knew that would be the answer. Steve

Link to this post | posted 09 Sep, 2020 01:38

scaruso

I am getting my students started using DNAM, online, of course, and one has run into a novel problem. I am sure it's something simple, but I sure can't figure out how they are getting this result. First they are running through a practice genome I use for training, and this student is getting a RBS results window that looks weird. I did ask if he is running DNAM as an administrator and if it had been updated. Anyone ever see this version of the RBS screen? Note that the column headers are wrong, no Z score, not final score. Thanks! Steve Edited 09 Sep, 2020 01:39 233Kb

Link to this post | posted 04 Sep, 2020 14:12
scaruso	Thanks, Debbie. Sorry to add to your plate. Never rains, but it pours. Steve

Link to this post | posted 04 Sep, 2020 12:30
scaruso	This is bad timing since I have 120 students blasting genes starting this weekend. Just to confirm, I checked it this morning on another computer and on the UMBC virtual desktop and got the same result. So it looks like either NCBI is having a problem or the connection between DNAM and NCBI has one. I did check NCBI online, and it is working, so it isn't the main BLAST system. Steve

Link to this post | posted 03 Sep, 2020 16:58
scaruso	Thanks, guess it's more than just me, then. Steve

Link to this post | posted 03 Sep, 2020 16:41
scaruso	I hope they are correct, although you never know. But I just got to campus and tried it from a computer that I know DNAM works on, and hasn't been changed. Same error. Steve

Link to this post | posted 03 Sep, 2020 15:14
scaruso	Tried it several times with different files and it never works. I have seen another error message, though: Error connect with SSL. EOF was observed that violates the protocol. Which sounds really unfortunate, if you ask me. Steve