X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=988c7112fc1109118f13ed6d45f160930d833dda;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=31a36f73c6d0339d775dd6a1a4efa8e523c0f14f;hpb=c48d91112209b841444923670dca5454da0e2a4d;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 31a36f7..988c711 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -38,7 +38,7 @@ string ChimeraCheckCommand::getHelpString(){
 	try {
 		string helpString = "";
 		helpString += "The chimera.check command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
-		helpString += "This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
+		helpString += "This command was created using the algorithms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
 		helpString += "The chimera.check command parameters are fasta, reference, processors, ksize, increment, svg and name.\n";
 		helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required unless you have a valid current fasta file. \n";
 		helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
@@ -628,11 +628,11 @@ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename)
 				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 = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
+				num = driver(lines[process], outputFileName + toString(m->mothurGetpid(process)) + ".temp", filename);
 				
 				//pass numSeqs to parent
 				ofstream out;
-				string tempFile = outputFileName + toString(getpid()) + ".num.temp";
+				string tempFile = outputFileName + toString(m->mothurGetpid(process)) + ".num.temp";
 				m->openOutputFile(tempFile, out);
 				out << num << endl;
 				out.close();