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Parsing location error (Read 17907 times)

Mar 2^nd, 2012 at 9:27pm

massimiliano Offline
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Posts: 8

I installed the last 64 bit release of UGENE in a linux mint 12 machine...when I import a genbank (.gb) file with the sequence and annotation this error message appear :"'Load document: 'TTN_human.gb'' task failed: Error parsing location"....and in the shell appear "Unknow property paddling". I had not this problem with the windows release. Any suggestions?
Thanks in advance
Max

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Reply #1 - Mar 5^th, 2012 at 5:40pm

Yuriy Vaskin Offline
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Posts: 138

Max, thank you for the report.

Could you please answer several questions:
1) Have you opened the same file on Windows?
2) Was it the latest UGENE version 1.10.3 (on Windows)?

Also, could you send us the "TTN_human.gb" file, because we can't reproduce the issue on other GenBank files?

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Reply #2 - Mar 5^th, 2012 at 11:02pm

massimiliano Offline
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Posts: 8

Hi,
thank a lot for replay...yes i opened the same files (and others Genbank files) in windows (same release 1.10.3)with no errors...anyway i send you an example file to test.
Thanks

titinb_danio.gb (184 KB | )

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Reply #3 - Mar 6^th, 2012 at 10:03pm

Yuriy Vaskin Offline
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Posts: 138

Max, we tried opening your file on windows and arch linux 64 bit. There was no problem with opening.

It seems that the file cannot be parsed because of your locale.
Could you please provide us with values of your environment variables? To do that just copy-paste an output of the "env" shell command here or send it on our email.

Thank you!

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Reply #4 - Mar 6^th, 2012 at 10:35pm

massimiliano Offline
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Posts: 8

Hi,
here the output of command "env" :

SSH_AGENT_PID=2119
GPG_AGENT_INFO=/tmp/keyring-2aWkG6/gpg:0:1
TERM=xterm
SHELL=/bin/bash
XDG_SESSION_COOKIE=11900a19ad1f34b8d9df2f2f00000007-1331018088.805971-409386575
GJS_DEBUG_OUTPUT=stderr
WINDOWID=52428805
GNOME_KEYRING_CONTROL=/tmp/keyring-2aWkG6
GJS_DEBUG_TOPICS=JS ERROR;JS LOG
GTK_MODULES=canberra-gtk-module:canberra-gtk-module
USER=max
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
SSH_AUTH_SOCK=/tmp/keyring-2aWkG6/ssh
SESSION_MANAGER=local/mint12:@/tmp/.ICE-unix/2073,unix/mint12:/tmp/.ICE-unix/207
3
USERNAME=max
DEFAULTS_PATH=/usr/share/gconf/gnome-shell.default.path
XDG_CONFIG_DIRS=/etc/xdg/xdg-gnome-shell:/etc/xdg
PATH=/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:
/sbin:/bin:/usr/games
DESKTOP_SESSION=gnome-shell
PWD=/home/max
GNOME_KEYRING_PID=2064
LANG=it_IT.UTF-8
MANDATORY_PATH=/usr/share/gconf/gnome-shell.mandatory.path
GDMSESSION=gnome-shell
SHLVL=1
HOME=/home/max
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
LOGNAME=max
XDG_DATA_DIRS=/usr/share/gnome-shell:/usr/share/gnome:/usr/local/share/:/usr/sha
re/
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-ihdB0Pqc8t,guid=06238a41f2adf6b
834e26aec00000039
DISPLAY=:0
XDG_CURRENT_DESKTOP=GNOME
COLORTERM=gnome-terminal
XAUTHORITY=/home/max/.Xauthority
_=/usr/bin/env

I also noticed that when i start UGENE from the shell appear this message: "QSslSocket: cannot resolve SSLv2_client_method
QSslSocket: cannot resolve SSLv2_server_method"
It coul be a problem?
Thanks for the help
Max

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Reply #5 - Mar 12^th, 2012 at 4:32pm

Yuriy Vaskin Offline
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Posts: 138

Max, sorry for the response delay.

We've tried the file on mint 12 with your locale, but it's been opened.

The file contains a couple of huge joined regions. Maybe that is the problem. Could you please open the attached files with UGENE on mint 12 and we'll see whether or not it is a problem with the joined regions.

P.S.
titinb_danio_no_join.gb has no joined regions.
titinb_danio_line_ends.gb has unix line ends (\r\n).

titinb_danio_no_join.gb (175 KB | )

titinb_danio_line_ends.gb (186 KB | )

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Reply #6 - Mar 12^th, 2012 at 5:58pm

massimiliano Offline
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Posts: 8

Hi Yuriy,
thanks a lot for the help.
When i try to open the file "titinb_danio_line_ends.gb" i have the usual error
"QSslSocket: cannot resolve SSLv2_client_method
QSslSocket: cannot resolve SSLv2_server_method
Unknown property paddling" and the file will not open.

Instead the other file is open without problem (i saw that it contains only the sequence withouth features like int/exon annotation,right?).

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Reply #7 - Mar 12^th, 2012 at 7:33pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Hi, Max
I've created an issue concerning the QSslSocket error (see https://ugene.unipro.ru/tracker/browse/UGENE-884).

Note that the other error ("Unknown paddling error") is a minor issue that can be ignored (you may see the following issue, for details: https://ugene.unipro.ru/tracker/browse/UGENE-880).

Could you please also test the attached file with one join left only.

Thanks,
Olga

titinb_danio_one_join.gb (176 KB | )

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Reply #8 - Mar 12^th, 2012 at 8:23pm

massimiliano Offline
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Posts: 8

Hi Olga,
yes this file works perfectly....i can see the mRNA sequence.
So the problem is the multiple joined regions? But why only using ugene under linux and not in windows?
Thanks
Max

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