According to runI-TASSER.pl, Step 2.4.1 should either be:
a) if homoflag = real ($run=real):
/bin/cp $plibdir/PDB/list ./list
b) if homoflag = benchmark ($run=benchmark) , go through a somewhat lengthy process of removing homologs
Documentation says that the default is "real".
However, if one does not specify homoflag, the output for step 2.4.1 is :
2.4.1 removing homology templates based on and 1
=> please remark the absence of "real" after "based on"
=> takes almost an hour, just like if I would use "-homoflag benchmark -idcut 1.0"
=> the end-result is a "list" file identical to $plibdir/PDB/list
If one specifies "-homoflag real":
2.4.1 removing homology templates based on real and 1
=> takes less than a second
if one specifies "-homoflag benchmark":
2.4.1 removing homology templates based on benchmark and 0.3
=> takes almost an hour to do "align" with all the PDB library
For now, I run it with "-homoflag real" to save almost an hour of CPU time...
Should line 12 in runI-TASSER.pl be uncommented? :
#$run="real"; #'real', use all templates; 'benchmark', homology will be removed