SEA-PHAGES | DNA master server down?

Link to this post \| posted 03 Jun, 2021 18:07
cdshaffer	Sometimes we just cannot see the simplest problems because we are concentrating so hard on the task at hand. You should try installing DNA Master on a Windows VM, not on an Ubuntu VM. There is a way to get Windows for free. I think the most recent instructions are here: https://phagesdb.org/media/docs/InstallingWindowsOnMac.pdf But if anyone knows of a more recent set of instructions please post.

Link to this post | posted 03 Jun, 2021 18:07

Sometimes we just cannot see the simplest problems because we are concentrating so hard on the task at hand.
You should try installing DNA Master on a Windows VM, not on an Ubuntu VM. There is a way to get Windows for free. I think the most recent instructions are here:

https://phagesdb.org/media/docs/InstallingWindowsOnMac.pdf

But if anyone knows of a more recent set of instructions please post.

Link to this post \| posted 03 Jun, 2021 20:38
rlb6	Thanks Chris, I did miss that step having more commonly worked on pc. I was able to install windows and then DNA Master. Unfortunately, I still don't have an error free copy of DNA Master as I'd hoped. Beckie Bortz

Link to this post \| posted 03 Jun, 2021 21:18
kcornely	Greetings, all! Thanks, Dan, your directions were super helpful. I noticed this recent post from Beckie in which she says that her copy of DNA Master is not "error-free". We are having some issues here as well. I have two new research students who installed DNA Master on their Macs in the emulator last week. I downloaded DNA Master on my new laptop (a PC), also last week. All three of us are having difficulties. I am having a problem updating DNA Master on my PC. I get an error message when I try to do so. My students are having similar update problems. Another problem that my students are having is that they are not able to BLAST individual genes (for example, when a different start choice is made). I've attached a screenshot so that you can see the error message my students are getting. Interestingly, there are no DNA Master difficulties on any computers on which DNA Master was installed sometime in the past. DNA Master works just fine on my home computer, my office computer, my lab computer and on the computers in the computer lab at the college. The problems we are having appear to be associated with recently-installed versions of DNA Master. Thanks in advance for any help you can provide! Kathleen 282Kb

Link to this post | posted 03 Jun, 2021 21:18

kcornely

Greetings, all!

Thanks, Dan, your directions were super helpful.

I noticed this recent post from Beckie in which she says that her copy of DNA Master is not "error-free". We are having some issues here as well. I have two new research students who installed DNA Master on their Macs in the emulator last week. I downloaded DNA Master on my new laptop (a PC), also last week. All three of us are having difficulties. I am having a problem updating DNA Master on my PC. I get an error message when I try to do so. My students are having similar update problems. Another problem that my students are having is that they are not able to BLAST individual genes (for example, when a different start choice is made). I've attached a screenshot so that you can see the error message my students are getting.

Interestingly, there are no DNA Master difficulties on any computers on which DNA Master was installed sometime in the past. DNA Master works just fine on my home computer, my office computer, my lab computer and on the computers in the computer lab at the college. The problems we are having appear to be associated with recently-installed versions of DNA Master.

Thanks in advance for any help you can provide!
Kathleen

Link to this post \| posted 03 Jun, 2021 21:35
debbie	Hi Kathleen, I am no expert, but the error is because DNA Master was written before the era of secure https. I believe that you are missing some SSL libraries. I had referred to these in the past, but I am not confident that they work. https://www.dropbox.com/sh/mtvey9ohuuykv7r/AADuZje-yHWf1SIRDE0eg9gVa?dl=0 His issue was then, where to put them. They are located in the main DNA Master folder on my computers (in Program files), so put them there. But, if that doesn't work or you like his advice better, here is another option. Christian Gauthier found the right stuff that worked for him here. For your future reference on this point, a lightweight program that folks can install to fix this issue is the Bitvise SSH Client (https://www.bitvise.com/ssh-client-download). Apparently it puts everything in the right place because DNA Master is now performing remote BLAST jobs without complaint! Fingers crossed! debbie Edited 03 Jun, 2021 21:36

Link to this post | posted 03 Jun, 2021 21:35

debbie

Hi Kathleen,
I am no expert, but the error is because DNA Master was written before the era of secure https.
I believe that you are missing some SSL libraries.

I had referred to these in the past, but I am not confident that they work.
https://www.dropbox.com/sh/mtvey9ohuuykv7r/AADuZje-yHWf1SIRDE0eg9gVa?dl=0

His issue was then, where to put them. They are located in the main DNA Master folder on my computers (in Program files), so put them there.

But, if that doesn't work or you like his advice better, here is another option.

Christian Gauthier found the right stuff that worked for him here.

For your future reference on this point, a lightweight program that folks can install to fix this issue is the Bitvise SSH Client (https://www.bitvise.com/ssh-client-download).

Apparently it puts everything in the right place because DNA Master is now performing remote BLAST jobs without complaint!

Fingers crossed!
debbie

Edited 03 Jun, 2021 21:36

Link to this post \| posted 09 Jun, 2021 15:26
scaruso	Can I ask a dumb question? I have students who are trying to download this for their PCs now and can't on any browser. And not for a virtual machine. Is it simply not possible to access DNA Master anymore without significant effort? Steve

Link to this post \| posted 09 Jun, 2021 15:39
scaruso	My computer is about to be reformatted, as it happens, which means I am about to loose DNAM. Any chance someone could send me a copy of DNAM or something? I kind'a need a working copy desperately. Steve

Link to this post \| posted 09 Jun, 2021 15:49
debbie	Steve, I think that Pitt servers were down for a bit this am. Here is the install download. https://www.dropbox.com/sh/ygbayg8zqy32wiq/AADM8F9-RXkkSYXVFA-hhhPza?dl=0

Link to this post \| posted 09 Jun, 2021 23:22
scaruso	Thank you! Steve

Link to this post \| posted 14 Jun, 2021 20:29
rlb6	Regardless of whether I get the program from the FTP server or from the dropbox link, the installation of DNA Master is creating errors. Once I install and update, I get an "error creating fields", the program tries to "update helpers", and ends with "FTP failures". I enlisted help from Kristen and the same errors were obtained with a new installation on her machine. She tried turning off firewalls but this did not resolve the issue. DNA Master seems to essentially be working in this state but can't access data outside the program such as Blast or to pull in genomes for comparison. I am unaware what else may be affected. The Bitvise SSH client may be a solution to pull in all of the files correctly, but I am not savvy enough to know how to make it work. Any help is appreciated! I hope this info helps to trouble-shoot this error and generate a reliable fix before a large number of students require it. Beckie Bortz

Link to this post | posted 14 Jun, 2021 20:29

rlb6

Regardless of whether I get the program from the FTP server or from the dropbox link, the installation of DNA Master is creating errors. Once I install and update, I get an "error creating fields", the program tries to "update helpers", and ends with "FTP failures". I enlisted help from Kristen and the same errors were obtained with a new installation on her machine. She tried turning off firewalls but this did not resolve the issue. DNA Master seems to essentially be working in this state but can't access data outside the program such as Blast or to pull in genomes for comparison. I am unaware what else may be affected. The Bitvise SSH client may be a solution to pull in all of the files correctly, but I am not savvy enough to know how to make it work. Any help is appreciated!

I hope this info helps to trouble-shoot this error and generate a reliable fix before a large number of students require it.

Beckie Bortz

Link to this post \| posted 23 Jun, 2021 14:55
scaruso	I have noticed that students and TAs with newer devices are running into problems downloading, even if I put it in a Google Drive, or running it if they can. They get error messages, sometimes that it is infected with a virus, sometimes others. I am no computer science person, but is it possible that the software of newer computers has moved past an older program and is causing problems that is going to get worse and worse? If so, do we have any ideas of how to proceed if we loose DNA Master? Steve

Link to this post | posted 23 Jun, 2021 14:55

scaruso

I have noticed that students and TAs with newer devices are running into problems downloading, even if I put it in a Google Drive, or running it if they can. They get error messages, sometimes that it is infected with a virus, sometimes others.

I am no computer science person, but is it possible that the software of newer computers has moved past an older program and is causing problems that is going to get worse and worse? If so, do we have any ideas of how to proceed if we loose DNA Master?

Steve

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DNA master server down?