check exit code of every subcommand; use xargs

[sapojnik]

1. to avoid the puzzling instability of results, check exit code of every subcommand, however simple
   (use sub systemF() rather than system(), use "or die" in other places);
2. use xargs to avoid shell failures on extra-long command lines that cannot be executed directly
   (needed for sequences over 100-200 Mbp)