runLOMETS.pl does not recognized the setting of -homoflag to real, although doc says default is real.
command : runLOMETS.pl -homoflag real ...
output :
Your setting is:
...
-homoflag =benchmark
-idcut =0.3
...
The following bold line in runLOMETS.pl seems to be the problem :
$run = "benchmark";
if(!$run)
{
$run="real"; #'real', use all templates; 'benchmark', homology will be removed
}
if($run eq "benchmark" && !$id_cut)
{
$id_cut=0.3; #cut-off of sequence idendity
}
elsif(!$id_cut)
{
$id_cut=1.0; #cut-off of sequence idendity
}
if($run eq "real" && $id_cut<1.0)
{
$id_cut=1.0;
}
If I comment this line, "-homoflag real" is recognized.