UGENE Forum - Reload after alignment

Sep 1^st, 2011 at 4:47pm

stephane roche Offline
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After multiple alignment, I need to unload and reload the file. Does it possible to do it automatically ?
Best Regards
Stephane

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Reply #1 - Sep 2^nd, 2011 at 1:51pm

Konstantin Okonechnikov Offline
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Posts: 173

Hi Stephane,
could you please describe your use case in detail? Why do you have to unload and reload the file? Do you modify the alignment by some external tool?

If you use UGENE's integrated algorithms or editing operations the alignment should be updated automatically.

If the file was modified by some external program then you should be asked if you would like to reload it. If it doesn't happen, something is wrong.

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Reply #2 - Sep 7^th, 2011 at 5:27pm

stephane roche Offline
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Dear Konstantin,
I use a Fasta file with multiple sequence. I add the file to the project. And do an alignment with an external tool (MUSCLE). When the alignment is done, I have no notification and no info in the log file.
To see the alignment, I need to close multiple sequence viewer, unload file and reload file.
I work with Windows 7 64bit PC, UGENE 1.9.6.
Stephane

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Reply #3 - Sep 7^th, 2011 at 6:39pm

Mikhail Fursov Offline
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All alignment algorithms run from UGENE viewers must update the viewed data automatically. If not - this is very critical issue.

Could you check the following

1) Open your file in MSA editor. Ensure that the corresponding element in Project View has black color

2) Align your file from MSA editor. Once finished check the Project View item has become blue (it means that the alignment is modified or updated)

?

The issue with a bad logging is also worth of extra bug in our system. Please check this one to know when the fix is ready: https://ugene.unipro.ru/tracker/browse/UGENE-585

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UGENE team

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Reply #4 - Sep 7^th, 2011 at 7:17pm

stephane roche Offline
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Hello,
When the file is newly open, it become black in the project viewer.

When I do alignment, I have just this message :
"[INFO][14:04] Saving document C:/Users/STPHAN~1/AppData/Local/Temp/EO2240.fa
[INFO][14:04] Saving document E:/Documents/Projets/Splicing FAT1/Séqeuncage/Organes/Seq 1 backup - Copie (2).fa "

and nothing else. In my opinion, it correspond well to the issue you forward.

After alignment, I see nothing in the project viewer. The file do not become blue.
But if I modify the file with a text editor, by adding of "return" at the end of a sequence name. The software detect well the modification and upgrade the MSA view, with the alignment.

The file in the project viewer do not become blue, it stay Black.

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Reply #5 - Sep 7^th, 2011 at 8:36pm

Mikhail Fursov Offline
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This is looks strange to me, I use the same version and OS and alignment with MUSCLE does work.

Lets check this with the file in attachment using the following scenario
1) open this file as alignment
2) insert space before the C letter
3) run alignment with muscle algorithm

The file must be realigned to initial state before the space is inserted and file name in the project view must be in dark blue color, but not black.

Could you check this scenario please?

test.fa (0 KB | )

---
UGENE team

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Reply #6 - Sep 12^th, 2011 at 7:55pm

stephane roche Offline
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Posts: 7

I have done your scenario and I have the problem previously describe, without actualization of the data.

I have no problem with MUSCLE algorithm. It works well, in every case. And I have the same problem with Clustal algorithm.

I have checked the modification date of the file. No problem again.

My Windows 7 Pro is a french version and not US version.
Stephane

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Reply #7 - Sep 12^th, 2011 at 9:11pm

Mikhail Fursov Offline
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Just tried the same file and ClustalW algorithm and it works well.

If you have problem with ClustalW algorithm, probably the issue depends on data set you are using. Could you please send us any data sample that can be used to reproduce the problem?

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UGENE team

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Reply #8 - Sep 12^th, 2011 at 11:54pm

Konstantin Okonechnikov Offline
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Posts: 173

Mikhail,
as I understood the problem occurred with the file you provided in this thread (test.fa). Stephane, please correct me if I'm wrong.

There is one more thing that might be helpful - UGENE application log.
Stephane, could you provide the full log output?

To access the full log do the following:

1) Open Settings->Prefrences. Then choose Logging page and make sure all Log categories are selected (as on screenshot 1)

2) Repeat the problematic alignment scenario with ClustalW without reloading the file

3) Click on Log button in bottom part of the UGENE window. In the Log view press Ctrl+A to select all text. Now you can copy it and paste into text file. (screenshot 2)

screenshot1.gif (20 KB | )

screenshot2.gif (34 KB | )

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Reply #9 - Sep 13^th, 2011 at 6:58pm

stephane roche Offline
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Posts: 7

Konstantin,
Yes, I have the problem with the test file.

I have copy the log into 2 files. In the first file, I have done alignment followed by a manual modification of the file after alignment in order to actualize the multiple alignment window. In the second file, I have done no manual modification in the file, just MUSCLE alignment followed by CLUSTAL alignment.

Stephane

log_ugene_test.txt (68 KB | )

log_ugene_test_without_reload.txt (54 KB | )

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Reply #10 - Sep 22^nd, 2011 at 10:16am

Konstantin Okonechnikov Offline
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Posts: 173

Stephane,
unfortunately the log was not detailed enough to understand the problem.

Recently we've released 1.9.7. In this release we improved logging of the alignment process significantly. Could you please install the new version and record the log again?

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Reply #11 - Sep 23^rd, 2011 at 2:31pm

stephane roche Offline
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Posts: 7

I will do it
Thanks
Stephane

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