mv: cannot stat file error when running 3D-Coffee

[Kenta Renard]

Dear Cedricc

I have been using 3D-Coffee perfectly fine when suddenly I get errors like:

mv: cannot stat 'file.1511.72765336049.237864': No such file or directory
mv: cannot stat 'file.48960.2782837213.237872': No such file or directory

When I use _SELF_P_, none of the sequences in the FASTA file recognise the .pdb files in the same directory with the same name. When I make a template file, the error persists. T-COFFEE manages to retrieve the FASTA input I have no issue. The command line is the same to ones I used before but with just changes to the input file and output file names:

t_coffee input.fasta -method sap_pair,slow_pair,mustang_pair -template_file _SELF_P_ -output fasta -outfile input_sapPair-SlowPair-MustangPair.fasta -multi_core -n_core 2]

Could you please help?

Best wishes,

Kenta

[Cedric Notredame]

Dear Kenta,

the "-" in the file name look like they could break something somewhere. It may be safer to remove them, or change them for "_"

Cheers,
Cedric

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

[Kenta Renard]

Dear Cedric,

I used "-" in the same before and it worked. When I ran an old command line that worked, it gave the same error. Any ideas?

Best wishes,

Kenta

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[Kenta Renard]

Dear Cedric,

Whatever file name I use, I still have the same issue. I used "-" in file names before and had no issue.

Best wishes,

Kenta

[Cedric Notredame]

Thank you Kenta

There is one thing I do not entirely understand. Is it a situation where some stuff that used to work stopped working, all things being apparently the same?

If that is the case, here are a couple of suggestions:

The handling of structural information sometimes requires network access and some pdb lookup. It may be that these access have changed on your side. 

I also think one of the lookup file that we get from rscb changed recently. This file gets updated when too old and it could be the culprit. Maybe it would make sense your remove the .t_coffee folder ( in your home directory by default) and do a clean install with the latest beta. 

I am suggesting this because t_coffee stores some online file for lookup and maybe some corruption happened there. 

If none of these work, pm me with sample files and command lines you are using and we will look into this. 

Cheers 

Cedric 

-- 

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

On 29 Nov 2024, at 11:53, Kenta Renard <kenta...@gmail.com> wrote:



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