with "while(<$handle>) {chomp; $self->{'logger'}->warn($_)}:"
-------------------------------------------------------------------------------

+ works for 12Tx432C.nex
+ works for 49Tx253C.nex
+ works for 500Tx759C.nex
+ Corba communication errors for large datasets: 7180Tx1359C.nex & 11361Tx1360.nex:
  java.net.SocketException: Broken pipe...
  2364 WARN CORBA.BOA.Client[undef] - Invalid GIOP header: magic="GIOP" message_size=19558596
+ timeout doesn't work
  

comment out "while(<$handle>) {chomp; $self->{'logger'}->warn($_)}:"
-------------------------------------------------------------------------------
+ works for 12Tx432C.nex
+ works for 49Tx253C.nex
+ mrbayes never launched for 500Tx759C.nex: (same problem as before):
+ Corba communication errors for large datasets: 7180Tx1359C.nex & 11361Tx1360.nex:
  java.net.SocketException: Broken pipe...
  2364 WARN CORBA.BOA.Client[undef] - Invalid GIOP header: magic="GIOP" message_size=19558596
+ timeout seems to work