Spaces in fully qualified path to executable cause t_coffee to fail
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If t_coffee is installed in a directory where the path contains a space and the fully qualified path is passed on the command line as such:
/Applications/Genetic\ Software/t_coffee -infile TCoffeeInput15_Mar_04_15_23_30_1 -outfile TCoffeeOutput15_Mar_04_15_23_30_2 -newtree TCoffeeInput15_Mar_04_15_23_30_1.dnd -output fasta_aln -type PROTEIN -dp_mode myers_miller_pair_wise
t_coffee fails internally to handle the space in argv[0] with the following error:
--ERROR: : Software/t_coffee does not exist [FATAL]
*************************************************************************************************
* FULL TRACE BACK PID: 68544
68544 -- ERROR: : Software/t_coffee does not exist [FATAL]
T-Coffee, like many linux tools does not support white spaces in PATH. I would suggest you avoid these things as they are very liley to result in issues, with either T-Coffee or other tools.
Furthermore, even if we were trying to fix it on T-Coffee. Since some the options rely on third party tools - most of which do not accept white spaces - the problem would most likely remain.