Re: T-Coffee Accurate fails

[Paolo Di Tommaso]

Hi Gerald, 

About the SAP warning I don't have a precise idea of what is happening. 

Maybe somebody else in the group knows more about it and can help you. 

Regarding the "Corrupted Lock System" error message it is a bug that we have tried to fix recently. I would suggests the following: 

1) check if in your environment is defined a variable named LOCKDIR_4_TCOFFEE.It defines the path where T-Coffee creates temporaries lock files. 

2) If this path exists, make it sure that it empty (does not contain any file).

3) If not exists, create this variable referring a path where T-Coffee can create that files e.g. export LOCKDIR_4_TCOFFEE="~/.t_coffee/locks"

It nothing of the above solve the problem, download and install the latest T-Coffee beta available here 

http://www.tcoffee.org/Packages/Beta/Latest/

Cheers,

Paolo

  

On Aug 1, 2011, at 6:13 PM, Schoenknecht, Gerald wrote:

Cedric, Paolo,

 

Using T-Coffee 8.99 on an iMac or MacBookPro using the ‘accurate’ mode I routinely get error messages like, “31956 -- WARNING: SAP failed to align: 7REQC.pdb against 7REQC.pdb [T-COFFEE:WARNING]”. It seems the alignment is entirely based on profiles not using structural information at all? Any idea?

 

This morning, using a set of sequences where a lot of structural information should be available, to program ‘hang up’ with “pid 78616 – Corrupted Lock System”. An alignment with MCoffee worked fine, but the ‘Accurate’ mode currently does not seem to work?

 

Best,  Gerald

 

*****************************************

Dr. Gerald Schoenknecht

Oklahoma State University

Dept. of Botany

104 Life Sciences East

Stillwater, OK 74078-3013, USA

gerald.sc...@okstate.edu

Phone: +1-405-744-5549

http://botany.okstate.edu/people_research/schoenk/index.html

*****************************************

 

[Cedric Notredame]

Dear Gerald,

The SAP warning has to do with sap unable to handle pairs of identical
PDBs 7REQC.pdb against 7REQC.pdb

This situation arises when two sequences get assigned the same template.
In that case, it makes no sense to do the template alignment, hence the
reliance on a non structure based method.

If the best template is the same for all your sequences, then it makes
sense that the alignment ends up being sequence only alignments (I do
not recommend using fugue)

Cheers,

Cedric

On 2/8/11 10:40 AM, Paolo Di Tommaso wrote:
> Hi Gerald,
>
> About the SAP warning I don't have a precise idea of what is happening.
>
> Maybe somebody else in the group knows more about it and can help you.
>
> Regarding the "Corrupted Lock System" error message it is a bug that we
> have tried to fix recently. I would suggests the following:
>
> 1) check if in your environment is defined a variable named
> LOCKDIR_4_TCOFFEE.It defines the path where T-Coffee creates temporaries
> lock files.
> 2) If this path exists, make it sure that it empty (does not contain any
> file).
> 3) If not exists, create this variable referring a path where T-Coffee
> can create that files e.g. export LOCKDIR_4_TCOFFEE="~/.t_coffee/locks"
>
> It nothing of the above solve the problem, download and install the
> latest T-Coffee beta available here
>
> http://www.tcoffee.org/Packages/Beta/Latest/
>
>
> Cheers,
> Paolo
>
>
> On Aug 1, 2011, at 6:13 PM, Schoenknecht, Gerald wrote:
>
>> Cedric, Paolo,

>> Using T-Coffee 8.99 on an iMac or MacBookPro using the �accurate� mode
>> I routinely get error messages like, �31956 -- WARNING: SAP failed to
>> align: 7REQC.pdb against 7REQC.pdb [T-COFFEE:WARNING]�. It seems the

>> alignment is entirely based on profiles not using structural
>> information at all? Any idea?
>> This morning, using a set of sequences where a lot of structural

>> information should be available, to program �hang up� with �pid 78616
>> � Corrupted Lock System�. An alignment with MCoffee worked fine, but
>> the �Accurate� mode currently does not seem to work?

>> Best, Gerald
>> *****************************************
>> Dr. Gerald Schoenknecht
>> Oklahoma State University
>> Dept. of Botany
>> 104 Life Sciences East
>> Stillwater, OK 74078-3013, USA

>> gerald.sc...@okstate.edu <mailto:gerald.sc...@okstate.edu>

>> Phone: +1-405-744-5549
>> http://botany.okstate.edu/people_research/schoenk/index.html
>> *****************************************
>

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--
##########################################
Dr Cedric Notredame
Group Leader
Notredame's lab - Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Room 440.03

Centre de Regulacio Genomica (CRG)
Dr. Aiguader, 88
08003 Barcelona
Spain

Ph# + 34 93 316 02 71
Fax# + 34 93 316 00 99
Mobile# + 34 66 250 47 82

email cedric.n...@crg.eu
url www.tcoffee.org
blog cedricnotredame.blogspot.com
ResearcherID: G-3868-2010
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