#15 T-Coffee/SAP hangs on long input pdb path names

closed-fixed
Biskit.Mod (17)
5
2007-07-31
2007-07-17
No

The third t-coffee step in the Aligner.py protocol hangs if the input PDB files are located in a folder that is deeply nested in the directory structure.
Either T-Coffee or SAP seems to have a threshold for the length of -P/some/file.alpha kind of input (at around 200 characters for all combined). This can become an issue with the validation step of Biskit.Mod.

Error Trace:
------------
...
Running t_coffee ..
-in P/procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/templates/t_coffee/1J55_A.alpha P/procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/templates/t_coffee/1K2H_A.alpha P/procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/templates/t_coffee/1K8U_A.alpha P/procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/templates/t_coffee/1KSO_A.alpha P/procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/templates/t_coffee/1M31_A.alpha P/procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/templates/t_coffee/1MHO_.alpha P/procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/templates/t_coffee/1MQ1_A.alpha P/procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/templates/t_coffee/1MWN_A.alpha P/procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/templates/t_coffee/1NSH_A.alpha Msap_pair -out_lib /procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/t_coffee/sap_pair.lib -output fasta_aln -outfile /procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/t_coffee/struct.aln -template_file No -newtree /procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/t_coffee/sequence.dnd -quiet /procsys/Lab_Luis_Serrano/Raik_Gruenberg/temp/project/validation/1DT7/t_coffee/t_coffee.log_3 -weight 1000

******************************************************************
* Job NOT Completed:[T-COFFEE, Version_5.05]
* Please CHECK:
...

Workaround:
-----------

Put the project into a folder closer to the root.

Discussion

  • Raik Gruenberg

    Raik Gruenberg - 2007-07-31
    • status: open --> open-fixed
     
  • Raik Gruenberg

    Raik Gruenberg - 2007-07-31

    Logged In: YES
    user_id=589508
    Originator: YES

    path names are now made relative to the t-coffee folder.

     
  • Raik Gruenberg

    Raik Gruenberg - 2007-07-31
    • status: open-fixed --> closed-fixed
     

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