1. See http://ugene.unipro.ru/forum/YaBB.pl?num=1326766085/15.
The user wrote: "What i did is I just remove fof URL parameter and hardcode fof file path in Execution String:
ttuner -if /home/kenson/Downloads/ABI/forward/fofn.txt -sa $outfile
instead of:
ttuner -if $fof -sa $outfile"
2. Also, on Windows there is the following problem with the URL parameters: the '\' characters in an URL path are modified to '/' and the command is not launched. Note that if the command is launched in the command line, then the error is "The syntax of the command is incorrect." occurs.
See also: UGENE-812