SEA-PHAGES | All posts created by kbutela

Link to this post \| posted 27 Mar, 2025 15:22
kbutela	hnance@ccga.edu Hi all, Anyone having a hard time getting DNA Master to update? This isn't for a new installation, just a regular update and shut down. On multiple computers on campus, the program won't update and either shuts down while trying to update or must be shut down using Task Manager in Windows. The program seems to work fine, otherwise. Thanks! Holly The DNA Master update server is currently down as of 3/27/2025. As long as you have version 5.23.6, build 2705, 24 October 2021, you do NOT need to update DNA Master. I'd recommend turning off automatic updates by navigating to Preferences –> Timed Events and unchecking the "Automatic checks for DNA Master updates" box.

Link to this post | posted 27 Mar, 2025 15:22

hnance@ccga.edu
Hi all,
Anyone having a hard time getting DNA Master to update? This isn't for a new installation, just a regular update and shut down. On multiple computers on campus, the program won't update and either shuts down while trying to update or must be shut down using Task Manager in Windows. The program seems to work fine, otherwise.
Thanks!
Holly

The DNA Master update server is currently down as of 3/27/2025. As long as you have version 5.23.6, build 2705, 24 October 2021, you do NOT need to update DNA Master. I'd recommend turning off automatic updates by navigating to Preferences –> Timed Events and unchecking the "Automatic checks for DNA Master updates" box.

Posted in: Bioinformatic Tools and Analyses → DNA Master not updating

Link to this post \| posted 13 Jan, 2025 18:42
kbutela	As of Monday 1/13 at 1:30 PM, the DNA Master server is working. It's been a while since DNA Master has needed an update, so as long as you have Version 5.23.6 build 2705 you are good to go. eagodin Hi Debbie, I'm having difficulty updating DNA Master on our school PCs - before I bring IT into the discussion, are there any issues with the server at this time? Thanks much, Liz

Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701

Link to this post \| posted 09 Jun, 2024 15:04
kbutela	Attached is the Cluster DI Report written at the SEA Faculty Meeting in June 2024. This Google Doc contains a draft list of cluster specific annotation tips drafted at the faculty meeting. 147Kb

Posted in: Cluster DI Annotation Tips → June 2024 Cluster DI Report and draft cluster specific annotation tips

Link to this post \| posted 14 Mar, 2024 15:35
kbutela	Hi Katie- Do you know what folders your university will enable you to download from, like Dropbox or Google Drive? Thanks, Kristen

Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701

Link to this post \| posted 27 Feb, 2024 19:09
kbutela	Marcie Warner and I have reviewed the frameshifts currently called in Cluster CZ4, and they are not matching up to any of the wet bench experimentally validated frameshift sequences listed in the Bioinformatics Guide. For now, we do not recommend calling frameshifts in this cluster until a more thorough investigation can be performed. The currently called slippery sequence is suspicious and may be an annotation error that has been propagated over the years.

Link to this post | posted 27 Feb, 2024 19:09

kbutela

Marcie Warner and I have reviewed the frameshifts currently called in Cluster CZ4, and they are not matching up to any of the wet bench experimentally validated frameshift sequences listed in the Bioinformatics Guide. For now, we do not recommend calling frameshifts in this cluster until a more thorough investigation can be performed. The currently called slippery sequence is suspicious and may be an annotation error that has been propagated over the years.

Posted in: Frameshifts and Introns → Frameshift in CZ4 Phage Annalisa

Link to this post \| posted 02 Jan, 2024 22:17
kbutela	I am piloting the Whisky application on my M2 Mac, Sonoma 14.0. I can confirm the auto annotation errors, although everything else seems to be working. There is a brief lag time in performing some operations. This may be a viable solution for students who can't install a VM on their Mac.

Posted in: DNA Master → DNA Master on M1 Mac

Link to this post \| posted 02 Jan, 2024 22:14
kbutela	As of 1/2/2024, the DNA Master server is online. You can use the original installation protocols in the Bioinformatics Guide.

Posted in: Bioinformatic Tools and Analyses → DNA Master not updating

Link to this post \| posted 02 Jan, 2024 22:12
kbutela	The DNA Master update server is back online as of 1/2/2024, so there is no need to perform the workaround solution on this page.

Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701

Link to this post \| posted 11 Aug, 2023 14:14
kbutela	For the time being, all new installations of DNA Master need to follow the instructions on this forum post in order to manually update: https://seaphages.org/forums/topic/5577/. You'll find all of the download links in that post. Since you've already been successful in installing DNA Master, you can skip ahead to the step "Locate the DNA Master folder where you installed the program; have it open in a finder window" and go from there. Good luck! If you have any questions on the new installation/update process, please post them on the linked forum post so everyone who may need help in the future can follow the questions and solutions in one place. I'm monitoring that forum more closely and can respond a little quicker if people need help. clfleischacker I just installed DNA Master on my new personal computer and the 5.22.5 version was loaded. I tried to update and am receiving the FTP error. Should I contact Kristen? I am just finishing up a genome and can try using a different computer but I am hoping to resolve this issue on my new computer (Windows 11).

Link to this post | posted 11 Aug, 2023 14:14

kbutela

For the time being, all new installations of DNA Master need to follow the instructions on this forum post in order to manually update: https://seaphages.org/forums/topic/5577/. You'll find all of the download links in that post. Since you've already been successful in installing DNA Master, you can skip ahead to the step "Locate the DNA Master folder where you installed the program; have it open in a finder window" and go from there.
Good luck! If you have any questions on the new installation/update process, please post them on the linked forum post so everyone who may need help in the future can follow the questions and solutions in one place. I'm monitoring that forum more closely and can respond a little quicker if people need help.

clfleischacker
I just installed DNA Master on my new personal computer and the 5.22.5 version was loaded. I tried to update and am receiving the FTP error. Should I contact Kristen? I am just finishing up a genome and can try using a different computer but I am hoping to resolve this issue on my new computer (Windows 11).

Posted in: Bioinformatic Tools and Analyses → DNA Master not updating

Link to this post \| posted 03 Aug, 2023 16:31
kbutela	Hi Martin- I have a few suggestions to help you troubleshoot your install. Before proceeding, make sure you are running DNA Master as an administrator. For some installations, DNA Master temporarily loses it's connection to the DMDB database folder, and it just needs to be relocated. To do this, check your preferences –> Local settings –> Directories. Look for the location of the Databases. It should point to wherever directory you saved DNA Master, something like C:\Program Files\DNA Master\DMDB\. Regardless of what it says, click on the "Browse" button and locate the DMDB folder in your DNA Master directory. This will tell DNA Master where the databases are and reset the connection. While you are in the Directories panel, it's probably a good idea to check all of your local settings to make sure they are correct. Click "Apply" to update your changes and "Ok." You can then close the preferences window. Exit and restart DNA Master, and then attempt to reopen your file. If this does not work, try to open a different dnam5 file. If you cannot open any files with DNA Master after resetting the location of your databases, then try uninstalling DNA Master and reinstalling the program using the instructions provided in this post. Because you are manually updating the program, make sure you move slowly through the "replace" and "merge" prompts. During my initial testing of this method, I found that one missed prompt can corrupt the installation process because files can get skipped. When you start the reinstalled program as an administrator, I'd again recommend double checking preferences again to make sure the correct directories are set. I had to reset my databases and helper program directories when I used this method, but some others don't. Hope this helps! mespariz Hi Kristen, I followed your steps and successfully obtained an updated version of DNA Master. However, I'm facing an issue when trying to open a previously saved dnam5 file. I'm receiving a "Database Failure" message, which is causing all the dnam5 files to appear empty. It seems like there might be a problem with the database. Could you please assist me in resolving this issue? Your help would be greatly appreciated. Thank you, Martín

Link to this post | posted 03 Aug, 2023 16:31

kbutela

Hi Martin-

I have a few suggestions to help you troubleshoot your install. Before proceeding, make sure you are running DNA Master as an administrator.

For some installations, DNA Master temporarily loses it's connection to the DMDB database folder, and it just needs to be relocated. To do this, check your preferences –> Local settings –> Directories. Look for the location of the Databases. It should point to wherever directory you saved DNA Master, something like C:\Program Files\DNA Master\DMDB\. Regardless of what it says, click on the "Browse" button and locate the DMDB folder in your DNA Master directory. This will tell DNA Master where the databases are and reset the connection. While you are in the Directories panel, it's probably a good idea to check all of your local settings to make sure they are correct. Click "Apply" to update your changes and "Ok." You can then close the preferences window. Exit and restart DNA Master, and then attempt to reopen your file.

If this does not work, try to open a different dnam5 file. If you cannot open any files with DNA Master after resetting the location of your databases, then try uninstalling DNA Master and reinstalling the program using the instructions provided in this post. Because you are manually updating the program, make sure you move slowly through the "replace" and "merge" prompts. During my initial testing of this method, I found that one missed prompt can corrupt the installation process because files can get skipped.

When you start the reinstalled program as an administrator, I'd again recommend double checking preferences again to make sure the correct directories are set. I had to reset my databases and helper program directories when I used this method, but some others don't. Hope this helps!

mespariz
Hi Kristen,

I followed your steps and successfully obtained an updated version of DNA Master. However, I'm facing an issue when trying to open a previously saved dnam5 file. I'm receiving a "Database Failure" message, which is causing all the dnam5 files to appear empty. It seems like there might be a problem with the database. Could you please assist me in resolving this issue? Your help would be greatly appreciated.

Thank you,
Martín

Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701

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