working of get.mimarkspackage and sra command

[mothur.git] / chimeraperseuscommand.cpp

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index b8d70c1b4c623c5a433da7334219af49a87fac00..ef3058d8cda30d8781e9a0057c9e93d77feeb1b9 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -1092,17 +1092,17 @@ int ChimeraPerseusCommand::createProcessesGroups(string outputFName, string accn
                
                //loop through and create all the processes you want
                while (process != processors) {
-                       int pid = fork();
+                       pid_t pid = fork();
                        
                        if (pid > 0) {
                                processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
                                process++;
                        }else if (pid == 0){
-                               num = driverGroups(outputFName + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", accnos + ".byCount." + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
+                               num = driverGroups(outputFName + toString(m->mothurGetpid(process)) + ".temp", accnos + toString(m->mothurGetpid(process)) + ".temp", accnos + ".byCount." + toString(m->mothurGetpid(process)) + ".temp", lines[process].start, lines[process].end, groups);
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = outputFName + toString(getpid()) + ".num.temp";
+                               string tempFile = outputFName + toString(m->mothurGetpid(process)) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                out << num << endl;
                                out.close();