SEA-PHAGES | All posts created by kbutela

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

Link to this post \| posted 27 Jul, 2023 20:59
kbutela	As of July 2023, we do not have sufficient HHPred evidence to confidently identify the tail assembly chaperone (TAC) genes in this cluster, so call them as "hypothetical proteins" without a frameshift for now. Older annotations may have called these genes as tail assembly chaperones using synteny, but newer research on TACs has shown that synteny alone is not sufficient evidence to make a functional determination of TAC for a gene. If you encounter matches to tail assembly chaperones in other annotated phages within this cluster or other clusters, look for Pham matches to Adjutor gp26 or Adjutor gp27. If the gene you are annotating is found in the same Pham as Adjutor gp26 or gp27, it should not be annotated as a tail assembly chaperone at this time.

Link to this post | posted 27 Jul, 2023 20:59

kbutela

As of July 2023, we do not have sufficient HHPred evidence to confidently identify the tail assembly chaperone (TAC) genes in this cluster, so call them as "hypothetical proteins" without a frameshift for now. Older annotations may have called these genes as tail assembly chaperones using synteny, but newer research on TACs has shown that synteny alone is not sufficient evidence to make a functional determination of TAC for a gene.

If you encounter matches to tail assembly chaperones in other annotated phages within this cluster or other clusters, look for Pham matches to Adjutor gp26 or Adjutor gp27. If the gene you are annotating is found in the same Pham as Adjutor gp26 or gp27, it should not be annotated as a tail assembly chaperone at this time.

Posted in: Cluster EF Annotation Tips → Tail assembly chaperones

Link to this post \| posted 13 Jul, 2023 20:49
kbutela	All- As of 7-13-2023, the Pitt server used to host DNA Master updates is still down due to firewall updates, and while we are making substantial progress on getting the server back online, this is an extremely complicated endeavor involving the efforts of multiple people, so we are asking for your patience while this issue is addressed. In the meantime, we have developed the following workflow for everyone to follow. If you have a functional copy of DNA Master (version 2701 or above), you do NOT need to update the program at this time. Please turn off your automatic updates by navigating to Preferences –> Timed Events and unchecking the box "Automatic checks for DNA Master updates every X days." Any "FTP Failure" error message that pops up while the server is down is more of an inconvenience at this time than anything else, and you can safely ignore them. If you need to install DNA Master on a new machine or uninstall a malfunctioning copy of DNA Master, you will need to update DNA Master using a workaround that will require you to install then manually update the program through copying and pasting files. The automatic DNA Master update would normally do this work behind the scenes for you, but because the server is down, you need to a bit of button pushing on your own. You will have a fully functional copy of DNA Master when you are finished. First, access my OneDrive folder containing the files that you will need. Please do not delete or move any of the files so that others can make use of the information. Next, download and install the "original" version of DNA Master using the dna master installer.exe file. Install normally using the instructions on PhagesDB and in the Bioinformatics Guide up until the point of updating the program. This will install the basic architecture needed to run DNA Master on your computer. Do not start DNA Master. This step is critical in the process, as the installer sets up the infrastructure needed on your computer to run DNA Master. You can't just copy my existing folder and run it on your machine; the installer must run first (believe me, I tried it.) Locate the DNA Master folder where you installed the program; have it open in a finder window. Download the "DNA Master Updated Program and Associated Files" folder from the OneDrive. This will take a few minutes and may download as a ZIP folder. Unzip the folder if needed. Copy all contents of this folder. Paste all contents from the DNA Master Updated Program and Associated Files folder into the DNA Master folder where you installed the program. You will get a series of popup windows asking if you want to merge or replace files. Hit merge when you get that option. If you only get replace, hit that option. This is the manual update process. You are now copying over all of the updated helper programs, database updates, version 2705 of DNA Master, and all associated information needed for DNA Master to properly function on your computer. After copying/replacing/merging is finished, you will notice that your DNA Master folder contains two versions of DNA Master: OldDNAMas.exe (do not use this one) and DNAMas.exe. You'll want to use DNAMas.exe. Do not delete any files or programs from the DNA Master folder. When finished, restart DNA Master. You may get a popup warning that DNA Master can't find the DMDB or Helper folders-this is normal, just redirect the program to the correct directories. Some folks get this error message when finishing the install but others do not. If you get the error-do not worry. DNA Master just needs to be pointed back to the correct location to it's DMDB database and Helper folders. You'll be prompted to those directories during the startup process. When things are back up and running, you'll see that you are now running version 2705. You can return to the setup guide and begin resetting your preferences. Be sure to turn off automatic updates while you are going through the preferences. I'm hoping that we can crowdsource any suggestions/troubleshooting tips as we work through this manual update process together, so please reply to this forum post if you have any issues or tips to share.

Link to this post | posted 13 Jul, 2023 20:49

kbutela

All-

As of 7-13-2023, the Pitt server used to host DNA Master updates is still down due to firewall updates, and while we are making substantial progress on getting the server back online, this is an extremely complicated endeavor involving the efforts of multiple people, so we are asking for your patience while this issue is addressed.

In the meantime, we have developed the following workflow for everyone to follow.

If you have a functional copy of DNA Master (version 2701 or above), you do NOT need to update the program at this time. Please turn off your automatic updates by navigating to Preferences –> Timed Events and unchecking the box "Automatic checks for DNA Master updates every X days." Any "FTP Failure" error message that pops up while the server is down is more of an inconvenience at this time than anything else, and you can safely ignore them.

If you need to install DNA Master on a new machine or uninstall a malfunctioning copy of DNA Master, you will need to update DNA Master using a workaround that will require you to install then manually update the program through copying and pasting files. The automatic DNA Master update would normally do this work behind the scenes for you, but because the server is down, you need to a bit of button pushing on your own. You will have a fully functional copy of DNA Master when you are finished.

First, access my OneDrive folder containing the files that you will need. Please do not delete or move any of the files so that others can make use of the information.

Next, download and install the "original" version of DNA Master using the dna master installer.exe file. Install normally using the instructions on PhagesDB and in the Bioinformatics Guide up until the point of updating the program. This will install the basic architecture needed to run DNA Master on your computer. Do not start DNA Master. This step is critical in the process, as the installer sets up the infrastructure needed on your computer to run DNA Master. You can't just copy my existing folder and run it on your machine; the installer must run first (believe me, I tried it.)

Locate the DNA Master folder where you installed the program; have it open in a finder window.

Download the "DNA Master Updated Program and Associated Files" folder from the OneDrive. This will take a few minutes and may download as a ZIP folder. Unzip the folder if needed.

Copy all contents of this folder.

Paste all contents from the DNA Master Updated Program and Associated Files folder into the DNA Master folder where you installed the program. You will get a series of popup windows asking if you want to merge or replace files. Hit merge when you get that option. If you only get replace, hit that option. This is the manual update process. You are now copying over all of the updated helper programs, database updates, version 2705 of DNA Master, and all associated information needed for DNA Master to properly function on your computer.

After copying/replacing/merging is finished, you will notice that your DNA Master folder contains two versions of DNA Master: OldDNAMas.exe (do not use this one) and DNAMas.exe. You'll want to use DNAMas.exe. Do not delete any files or programs from the DNA Master folder.

When finished, restart DNA Master. You may get a popup warning that DNA Master can't find the DMDB or Helper folders-this is normal, just redirect the program to the correct directories. Some folks get this error message when finishing the install but others do not. If you get the error-do not worry. DNA Master just needs to be pointed back to the correct location to it's DMDB database and Helper folders. You'll be prompted to those directories during the startup process.

When things are back up and running, you'll see that you are now running version 2705. You can return to the setup guide and begin resetting your preferences. Be sure to turn off automatic updates while you are going through the preferences.

I'm hoping that we can crowdsource any suggestions/troubleshooting tips as we work through this manual update process together, so please reply to this forum post if you have any issues or tips to share.

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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All posts created by kbutela