cdshaffer
just to document for anyone what wants to create an auto-annotation here is what I did:

1. open DNA Master and do the standard File -> Open Fasta and import the sequence
2. Go go https://discover.kbrinsgd.org/autoannotate/ and enter phage name and upload the same sequence file you used in step 1
3. Click "Process"
4. In the text box below the process button you will get the auto-annotation as "Documentation"; it will have a bunch of entries that look something like this:

CDS 15 - 272
  /gene="1"
  /product="gp1"
  /locus tag="Roots515_1"

5. Select and Copy the entire contents of that text box
6. Go back to DNA master, on the phage window click the "Documentation" tab at the top right
7. Delete any text in the large text box and paste in from the results from the PECAAN auto-annotation. (When I did this this step I got about 100 question marks at the end which I deleted so the last entry ended like this:

CDS join(155929. .156288;1. .1
  /gene="232"
  /product="gp232"
  /locus tag="Roots515_232"
    /note=Original Glimmer call @bp 155929 has strength 11.01 ** not called by GeneMark

8. click the parse button, then in the window that opens accept the defaults and click the new parse button. This will convert the "documentation" into DNA Master gene entries
9. Save the DNA Master file as usual

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.