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Genbank Format File Annotation not Loading Since 1.21 (Read 3483 times)
Apr 13th, 2016 at 11:29pm

tea   Offline
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Hi

Since I updated UGENE from 1.20 to 1.21, my genbank file annotation is gone. When I open it up with the notepad, the annotations are there but doesn't appear in the UGENE. I tried 1.22 and no luck. I rolled back to 1.20 and I can see the annotations again in UGENE. I attached one of my genbank file that had this problem, if you want to reproduce the same issue. I'm using 64-bit windows and installed the 64 bit full version. Any help will be appreciated.

Tea
 

pSAG1-mCherry.gb (13 KB | 153 )
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Reply #1 - Apr 18th, 2016 at 7:46pm

Olga Golosova   Offline
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Hi! I'm not able to reproduce the issue on my computer. The file is opened and all the annotations are shown in my 1.22 version of UGENE full package for Windows 64-bit (see the screenshot).

Have you tried to manually drag the annotations object to the opened sequence view in UGENE 1.22?

You might also try to reset all UGENE settings. To do it you should check the "Reset settings to default on the next run" option in the UGENE Application Settings and then restart UGENE (https://ugene.net/wiki/display/UUOUM22/General).
 

annotations.jpg (154 KB | 150 )
annotations.jpg
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Reply #2 - Sep 21st, 2016 at 6:21pm

Malvolio   Offline
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Hello!

Many thanks for the suggestion to drag the annotations, that also helped my issue. But if I reload the project file, the annotations are gone again.

I made some testing and here's how this may work:

* creating a local project file and adding local *.gb files there does not have this bug;
* however, in our lab the files are kept on a samba server, which I manually mount to my GNU/Linux machine;
* in this case if I open a samba-located project file with samba-located *.gb files the annotations do not load and have to be dragged by hand;
* to make things even more complicated I use symbolic links (but the problem seems to be specific to remote shares);

Some info on my PC:
Kubuntu 16.04.1, 64 bit
4 core Intel Xeon
Ugene 1.24.2 (from repository)
 
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Reply #3 - Sep 22nd, 2016 at 4:36pm

Olga Golosova   Offline
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Hello, Malvolio!

Thanks for the clear description of the scenario. I've created an issue about that in our tracker.

By the way, have you considered using UGENE shared storage for your lab? It is possible to organize your data by folders using the storage, see the data updated by another UGENE instance in real-time mode, etc.
 
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Reply #4 - Sep 23rd, 2016 at 1:36am

Malvolio   Offline
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Dear Olga,

thank you for opening the bug, I am always happy to help development of UGENE! Smiley

I know about the shared database feature and I find it really cool! Unfortunately, my boss is a little old-fashioned and wants to keep all data in plain file/folder structure. Still, I am planning to try it out on my local machine.
 
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Reply #5 - Sep 26th, 2016 at 4:14pm

Olga Golosova   Offline
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Malvolio,

Quote:
thank you for opening the bug, I am always happy to help development of UGENE! Smiley

You're welcome! We're always happy to get feedback, especially positive  Smiley

Quote:
I know about the shared database feature and I find it really cool! Unfortunately, my boss is a little old-fashioned and wants to keep all data in plain file/folder structure. Still, I am planning to try it out on my local machine.

OK, I see.
 
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Reply #6 - Nov 7th, 2016 at 1:04pm

Denis Kandrov   Offline
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Hello, Malvolio.

I tried to reproduce the bug, but all work as expected:
- I mounted samba shared folder:  # mount -t cifs //my-samba-server/misc /media/smb/
- I exported my project to folder on this samba server:  /media/smb/smb_test
- I created symlink to this folder in my home folder:  ln -s /media/smb/smb_test /home/ugene/smb_test
- Then I closed UGENE and unmounted samba share.
- And again I mounted samba shared folder and tried open project from my home folder. After that all .gb were opened with annotations. Also .fasta with related .gb files with annotations were opened.

May be your .uproj file was created by old version of UGENE? Can you try to save project to new file with new version of UGENE and try reproduce the issue?

 
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