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gb files with annotations from UGENE 1.14.0 could not be loaded in 1.14.1 (Read 6962 times)
Sep 21st, 2014 at 5:16am

MandatoryCookie   Offline
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I am experiencing the same issue that has already been reported before: UGENE-3485
Briefly, gb files downloaded via UGENE 1.14.0 with manually added annotations could no longer be opened with UGENE 1.14.1 with the error message:

Task {Load document: 'XXX.gb'} finished with error: The file contains an incorrect data that describes a qualifier value. The value cannot contain a single quote character. The qualifier is ' /translation="XXX"XXX"XXX"'

As a temporary solution I considered downgrading to version 1.14.0. However, it seems that this version have been removed from the ppa. Since it is one of the easiest method to install UGENE in linux, would you consider re uploading UGENE 1.14.0 in the launchpad until this issue will be resolved?

If not, maybe you can help me find earlier versions of UGENE on your site or give instructions on how to easily downgrade

Distro: Linux Mint 17 Qiana (64 bit)
UGENE: v1.14.1 (64-bit)
 
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Reply #1 - Sep 22nd, 2014 at 5:35pm

German   Offline
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Posts: 118
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Dear User,

We are very sorry for this inconvenience. The problem is that UGENE 1.14.0 and earlier versions generated Genbank files with a little mistake. We fixed this mistake for UGENE 1.14.1 and you see the results... You are right that we have planned to improve it and UGENE 1.14.2 will be able to open the "old" files.

Here is the link to UGENE 1.14.0 for Linux x64:
Standard: http://ugene.unipro.ru/downloads/ugene-1.14.0-x86-64.tar.gz
Full: http://ugene.unipro.ru/downloads/ugene-1.14.0-x86-64-full.tar.gz

Another solution is to fix these Genbank files you have. That little mistake was that a qualifier value can not contain quotes, and if you want to use quotes you should use double quotation (Genbank spec.). So, if you replace
/translation="XXX"XXX"XXX"
with
/translation="XXX""XXX""XXX"
UGENE would open the file.
 
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