SAP failed to align

[Kenta Renard]

Dear Cedric,

I had another issue. I am trying to do a structural alignment and I am getting the following error message:

pid 375295 -- SAP failed to align: model1.pdb against model2.pdb [model1 model2]- attempt 1 [WARNING:T-COFFEE]
sh: line 1: 376332 Segmentation fault      sap in1 in2 > sapout 2> /dev/null

The variables are as below:

export PLUGINS_4_TCOFFEE=/rds/general/user/kr3118/home/.t_coffee/plugins/linux
export LOCKDIR_4_TCOFFEE=/rds/general/user/kr3118/home/.t_coffee/lck
export TMP_4_TCOFFEE=/rds/general/user/kr3118/home/.t_coffee/tmp
export DIR_4_TCOFFEE=/rds/general/user/kr3118/home/.t_coffee
export CACHE_4_TCOFFEE=/rds/general/user/kr3118/home/.t_coffee/cache

What is causing this error?

Best wishes,

Kenta

[Kenta Renard]

I am also getting the error on another machine:

--ERROR: #  [FATAL:T-COFFEE]

# The Program A2BUK1 Needed by T-COFFEE Could not be found
# If A2BUK1 is installed on your system:
#            -Make sure A2BUK1 is in your $path:
# If A2BUK1 is NOT installed obtain a copy from:
#       (null)
#
#
# and install it manualy

This is strange because I used this version before just fine (Version_13.46.0.919e8c6b) and this never happened. I did not change anything.

Best wishes,

Kenta

[Cedric Notredame]

Hello Kenta

Please send us the files and command lines you have been using. But before this, I would recommend a clean install of the latest beta as suggested in my last mail. 

Best 

Cedric 

-- 

Dr Cedric Notredame, PhD
ORCID - https://orcid.org/0000-0003-1461-0988

On 1 Dec 2024, at 16:33, Kenta Renard <kenta...@gmail.com> wrote:



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