java -jar searchtermfrequency-1.0-SNAPSHOT.jar -output /netapp/marketing/logipages/searchterms.aggregate -input /netapp/marketing/logipages/2007/*/* 
 make sure there is no other files in netapp/marketing/logipages/2007/*/* besides the output of phase 1

or use an extension that uniquily identifies the files of the phase 1 final outputs and use ...2007/*/*.ext