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PHYLIP (Read 2030 times)
Sep 21st, 2016 at 6:24pm

Radovan   Offline
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Hello,

I just installed v.1.24.2 and just started making Phylogenic trees. Opened the COI file from CLUSTALW samples folder.
I tried to make Phylogenetic Tree with the default options

1. PHYLIP Neighbor Joining - gave error
[ERROR][13:18] Task {Calculating Phylogenetic Tree} finished with error: Subtask {PHYLIP command line wrapper task} is failed: Subtask {Run UGENE command line: --phylip} is failed: An error occurred. Process is not finished successfully.

2. MrBayes - gave error
[ERROR][13:20] Task {Calculating Phylogenetic Tree} finished with error: Subtask {MrBayes tree calculation} is failed: MrBayes tool exited with code 1

3. PhyML Maximum Liklehood - gave the tree!
[INFO][13:21] Task {Open new 'Phylogenetic tree viewer'} finished

Any comments would be appreciated,
Regards,
Radovan

EDIT:
Excuse me for not giving some more details.
I was using VirtualBox and VMware Player and Linux Mint (host). Then I installed Ugene on Win7 32bit and Win7 64 bit Virtual machines (even installing on Win7 64 bit will fail for me). It seems that the issue with errors in calculation is present when using virtual machines. I am not sure about it, but I've noticed that other calculating procedures (like multiple alignments with MUSCLE etc.) will sometime fail and sometimes not fail. I guess that Ugene does not like installing on Virtual machines.

Does anybody have similar experience with Virtual machines? 
« Last Edit: Sep 22nd, 2016 at 2:42pm by Radovan »  
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Reply #1 - Sep 23rd, 2016 at 1:27pm

Denis Kandrov   Offline
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Hello, Radovan!

From time to time I use UGENE on VirtualBox, but I didn't have similar experience.  Huh

Could you tell us parameters of your virtual machines?
  • number of cpus
  • volume of memory


And why do you try using UGENE on virtual machines? Why are you not using UGENE on native machine?
 
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Reply #2 - Sep 23rd, 2016 at 3:24pm

Radovan   Offline
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Hello Denis,

Thank you for answering on my post.  Smiley

I am using Virtual machines because I personally use Linux Mint, and I wanted to try Ugene for my colleagues who (of course) use Windows.

On the other hand, thank you for mentioning the number of CPU used, I changed it from 1 to 4 on my Win 7 64bit VMware and it seems that solved the problem for my Office computer.

But, unfortunately, I had to use 32 Ugene version (ugene2.png) because 64 bit version refused to start - it installed Ok but I could not start it. I do not know what was the reason of not possible use of 64 bit Ugene version.

When I used the 32 bit Ugene version (full insttall) I could repeat the calculations (multiple allignment) and get the Phylogenetic trees multiple times  Smiley.  (ugene3.png). Here appeared just a minor problem of not having permission to write to a folder (strange, because I started is as Adminisatrator??)

Anyway, It seems I can propose my colleagues to use Ugene and, at the same time, I can use it as well in my Virtual machines - this way or another.

Best Regards,
Radovan 
 

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Reply #3 - Sep 29th, 2016 at 12:03pm

Denis Kandrov   Offline
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Hello, Radovan.

Sorry for late response. Nice to hear about your wish to offer UGENE to your colleagues.  Smiley

You wrote:
"But, unfortunately, I had to use 32 Ugene version (ugene2.png) because 64 bit version refused to start - it installed Ok but I could not start it. I do not know what was the reason of not possible use of 64 bit Ugene version."
On which Virtual machine you try to execute 64bit version? On 32bit version of Windows 64bit program not works. It's normal.

We think about permissions to write, but currently we don't have good decision.

 
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Reply #4 - Jul 26th, 2018 at 5:50am

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Hi there....I'm using 1.29 version. I'm trying to do a Phylogenetic tree, but the system crash because the limit of 1536MBp, How I can to overcame this limitation? thanks in advance
 
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Reply #5 - Jul 26th, 2018 at 12:21pm

Olga Golosova   Offline
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Hi! What operating system do you have? Is it 32-bit or 64-bit? If it is 64-bit, please use 64-bit UGENE package as well. You may use the universal installer package to install it in this case.

The system should not crash anyway, even with 32-bit UGENE.. Could you please send us a screenshot?
 
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Reply #6 - Jul 27th, 2018 at 4:51am

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Hi! thanks for your soon answer.I have windows 7 but I tested with Windows 8 too. I couldn't install the 64 package. THe problem is in settings/resources/task momory limit, is 1536MBP It don't let you modify to 1559 MPBS as the program report in error message.
 

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Reply #7 - Jul 28th, 2018 at 1:30am

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Hi, I tryied to install 64 bits program and I couldn't.
 
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Reply #8 - Jul 30th, 2018 at 2:27pm

Olga Golosova   Offline
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Instead of using this UGENE version, you should install the software again, i.e.:
  • Download this installer
  • Launch it and follow the installation
  • Open the new installed UGENE and try to reproduce your scenario


If you have a problem doing that, please describe it in more details and provide a screenshot.
 
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Reply #9 - Jul 30th, 2018 at 7:26pm

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Hi, I installed again as you suggest. this new instalation, still has the Settings/resuources/1536mbp. Are there any way to overcome this resources limitation???
 

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Reply #10 - Jul 30th, 2018 at 7:29pm

Olga Golosova   Offline
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Please attach also a screenshot of the "About UGENE" dialog (the dialog is available from the "Help" main menu).
 
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Reply #11 - Jul 30th, 2018 at 10:09pm

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I can't load the screen, sorry. I reinstalled the program and selected 64 bits. But in "About" tells "Unipro Ugene v 1.30.0, May 2018, 32 bits version"
 
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Reply #12 - Jul 31st, 2018 at 3:01pm

Alexey Tiunov   Offline
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Hello, I'm a UGENE developer.

The limitation of available memory is because of limitation for 32-bit applications in Windows. 32-bit Windows can launch only 32-bit applications, 64-bit Windows can launch both 32-bit and 64-bit applications. I suspect that you have 32-bit Windows, because you had some troubles with installing 64-bit UGENE.
Could you please provide a screenshot with your OS properties? You can find it by opening "Computer" window and clicking "System properties" on the toolbar (see the attached screenshots).

If you have 32-bit Windows, then it is impossible to launch 64-bit UGENE. We can modify the code special for you to force launch PHYLIP even if there is not enough memory, but we can't guarantee that you'll receive a result. This limitation was added to avoid spontaneous application crashes.
If your computer is powerful enough, then 64-bit Windows is more preferable than 32-bit. You should have at least 2 Gb of RAM (Windows 7 system requirements).

If you have 64-bit Windows then you should just launch 64-bit UGENE. As I understand, you have 32-bit UGENE installed somewhere. Uninstall it to be sure that it doesn't interfere with 64-bit UGENE. You can do it with "Uninstall" menu item in Start menu. To be sure that everything it removed check that there are no folders "C:\Program Files\Unipro UGENE" and "C:\Program Files (x86)\Unipro UGENE".
Then download the following package: http://ugene.net/downloads/ugene_latest_win_x86_64_zip_full.html. It is not an installer, it is just an archive, so you won't have any troubles with the installation. Unpack it somewhere and launch "ugeneui.exe" from it. I recommend to use the online installer Olga offered in the previous post, but to avoid as much possible troubles as you can use this package.

Please notify us either if it solves your problem or if you still have troubles.
 

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