Re: ask for help, local use tcoffee error

[Paolo Di Tommaso]

Dear Jian, 

I was able to align your dataset with Expresso, so I think it should something missing in your environment (you may be interested to check the result here  http://tcoffee.crg.cat/apps/tcoffee/result?rid=e2ef971d) 

Looking at your environment variables it seems something is wrong with a couple of path used by T-Coffee for temporary data. 

I would suggests to the following: 

Add to your environment  (or update if already exist) the variables TMP_4_TCOFFEE and LOCKDIR_4_TCOFFEE making them to reference to a couple of path newly created. For example: 

export LOCKDIR_4_TCOFFEE=/home/yang/.t_coffee/lck
export TMP_4_TCOFFEE=/home/yang/.t_coffee/tmp

Also I would suggest to empty your T-Coffee cache directory, the path i.e. /home/yang/.t_coffee/cache

Let me know if this fix your problem. 

Cheers,

Paolo Di Tommaso

Software Engineer 

Comparative Bioinformatics Group

Centre de Regulacio Genomica (CRG)

Dr. Aiguader, 88

08003 Barcelona, Spain

Begin forwarded message:

From: Jian YANG <ya...@ipbcams.ac.cn>
Date: August 12, 2011 10:11:58 AM GMT+02:00
To: cedric.notredame <cedric.n...@europe.com>
Subject: ask for help, local use tcoffee error
Reply-To: "ya...@ipbcams.ac.cn" <ya...@ipbcams.ac.cn>

Dear Dr. Notredame,  

I installed your binary version of tcoffee(8.99) on local Linux system (SUSE 10).
Using the same dataset, if I use fast mode it works well. But if I use '-mode accurate' or 'expresso' error messages were sent. Attached is the ErrorReport it dumped. In addition, I found a 't_coffee' process was running in background and I can't kill it. It soon used up all CPU and caused system crash.
I don't know what wrong with my local system, could you please help me solve it since I have a large amount of data to be analysed by tcoffee.

Thank you in advance and look forward to hearing from you soon.


Sincerely,


Jian
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Jian YANG, PhD
Laboratory of Bioinformatics
Institute of Pathogen Biology, CAMS&PUMC
6 Rongjing Eastern Street, BDA
Beijing 100176 P.R.China
Tel: 86-10-67877735
Fax: 86-10-67877736
E-mail: ya...@ipbcams.ac.cn; ya...@ipb.pumc.edu.cn
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<t_coffee.ErrorReport>