UGENE Forum - Bootstrap in PHYLIP Neighbor Joining causes UGENE to crash in Ubuntu


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Bootstrap in PHYLIP Neighbor Joining causes UGENE to crash in Ubuntu (Read 18381 times)

Nov 7^th, 2011 at 10:46pm

Alvarenga Offline
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Hi! I just found out about UGENE and I think it's great! Congratulations, and thank you! I'm really looking forward for its community to grow and the software to keep receiving new features.

I'm using Ubuntu Linux 11.10 and I have installed v.1.9.8 from the iefremov ppa.

I tried to produce a NJ phylogenetic tree with UGENE and succeeded with bootstraping off, but turning bootstrap on (with any number of repetitions) results in UGENE crashing (the UI disapears). I tried using ClustalW and Muscle alignments with the formats .fasta and .aln and I always end up with the same crash. Running UGENE ui from the terminal results in the following message:

ERROR in user tree: duplicate name found: 00000

Does anyone have any idea about what's going on?

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Reply #1 - Nov 8^th, 2011 at 2:29pm

Yuriy Vaskin Offline
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Thanks for the report!
I've created a corresponding issue (https://ugene.unipro.ru/tracker/browse/UGENE-691).
But if you provide us with your alignment or just with the names of the sequences in the alignment or with a screenshot of the full names of the sequences in the alignment it will worth nothing to fix it. Otherwise it will be difficult to fix it because bootstrap works perfect on our test set and on all the alignments I've tried.

p.s. I realize that your alignment could be private but we have no interest in using it somehow except for fixing the problem. ugene@unipro.ru or my email: vaskin@unipro.ru works as well. Thank you!

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Reply #2 - Nov 8^th, 2011 at 7:57pm

Alvarenga Offline
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I'm sorry, I forgot to mention that I tested it both with my own alignments and with the sample nucleotide alignments from UGENE (COI.aln and HIV-1.aln) and they all resulted in the same error.

I'm running Ubuntu 11.10 32bit, but I also tested the UGENE v.1.9.8 from the same ppa in Ubuntu 11.04 64bit and I got the same errors.

I also have just ran into a segmentation fault while trying to run NJ once again in my machine, but I can't reproduce it. I'll keep trying.

I'm attaching the texts from the terminal for both errors. (Sorry, but the text returning with the segmentation fault was too long, so I could only retrieve the last part of it from the terminal).

Maybe it's an issue with Ubuntu?

duplicate_name_UGENE.txt (3 KB | )

segmentation_fault_UGENE.txt (22 KB | )

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Reply #3 - Nov 8^th, 2011 at 9:30pm

Yuriy Vaskin Offline
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Thank you, now it's much clearer.
Yeah, it seems that it crashes only in Ubuntu, because I can't reproduce the issue on Windows. I think it'll be fixed in the 1.10 version release.

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Reply #4 - Nov 18^th, 2011 at 3:43pm

Yuriy Vaskin Offline
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By the way. The problem has been fixed. To use bootstrap in Ubuntu you may download our development snapshot(http://ugene.unipro.ru/snapshot.html) or wait a bit for UGENE 1.10 release.

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Reply #5 - Dec 16^th, 2011 at 8:36pm

Alvarenga Offline
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I just tested UGENE 1.10 on the same machine and the problem really is gone. Once again, congratulations for everyone's great work in UGENE and thank you very much for fixing the bug, and so quickly! Cheers!

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