General Category >> Help and How-to >> MUSCLE couldn't finish the task

Message started by PAL on Jul 21st, 2011 at 6:20pm

Title: MUSCLE couldn't finish the task
Post by PAL on Jul 21st, 2011 at 6:20pm
Dear UGENE developers,

I am a new user of UGENE and I am very satisfied with the tools it handles.

I have a project with more than 200 sequences in fasta format and I would like to perform an alignment with MUSCLE. At the beginning it seems it was ok but then it crak and sends an error message. Is this a bug or am I doing something wrong?

Thanks in advance,

Title: Re: MUSCLE couldn't finish the task
Post by Agu on Jul 21st, 2011 at 10:19pm
Hi PAL. I'm stepping in, but I'm just a user.
I've been doing alignments this week, and I haven't had any problems with the current version of UGENE (1.9.4). Nevertheless, is difficult to know what happen in your case with so little information. What did the error say? Is ugene crashing? (showing the window where it offers to submit a report)
Does it happen every time you try to align? Also with other sequences or a small set?

Just for testing you could try to align only a few columns (Column range) and see what happens (this way it will be much faster).

If you can reproduce the error only with that set of sequences, then of course the best option (maybe not possible or pleasant) is to submit the files to test them...

Title: Re: MUSCLE couldn't finish the task
Post by Mikhail Fursov on Jul 21st, 2011 at 10:30pm
This is regression in UGENE and will be fixed with the next patch release (1.9.5)

Reason of the bug:
We have switched some internal computations recently to be executed in a separate UGENE process to make the GUI UGENE process more stable and do not depend on internal tools errors/crashes. The bug in process in/out check was recently identified that can cause this problem on one environment, while another will work OK.

And, yes, please send us the OS info and files you have if it is possible, as Agu said. So we can test the issue on your data sets too.

Title: Re: MUSCLE couldn't finish the task
Post by PAL on Jul 22nd, 2011 at 7:53pm
Hello again,

you are of course right, I forgot to post the error message.
Ive tried to do a new alignment with MUSCLE both using all sequences and positions, a subset of sequences and with a shortest column range, however the process always crack. The error message was in all the cases the following: "'MSAAlignMultiTask' task failed: Subtask {MUSCLE run in separate process align 'XXY.fas'} is failed: Undefined error: muscle task did not produced result".

When it will be released the next patch 1.9.5?

Thanks in advance

Title: Re: MUSCLE couldn't finish the task
Post by Konstantin Okonechnikov on Jul 23rd, 2011 at 11:29am
1.9.5 is planned to be released on Monday, July 25.

BTW, you can try using latest unstable version, the bug is already fixed in the snapshot:

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