X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=80698f1b4b0317719421dbe9c4af3c0583bd9d97;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=b793dc885ef9213f290f118be55066a0e2837086;hpb=7f1aca4ed9e6db70de82e80ca4771f7680b21d26;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index b793dc8..80698f1 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -458,7 +458,7 @@ int TreeGroupCommand::execute(){
                 readMatrix->read(nameMap);
             }else if (countfile != "") {
                 ct = new CountTable();
-                ct->readTable(countfile);
+                ct->readTable(countfile, true);
                 readMatrix->read(ct);
             }else {
                 readMatrix->read(nameMap);
@@ -662,8 +662,18 @@ int TreeGroupCommand::makeSimsShared() {
             
             if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
         }
-        
         numGroups = lookup.size();
+        
+        //sanity check to make sure processors < numComparisions
+        int numDists = 0;
+        for(int i=0;i<numGroups;i++){
+            for(int j=0;j<i;j++){
+                numDists++;
+                if (numDists > processors) { break; }
+            }
+        }
+        if (numDists < processors) { processors = numDists; }
+        
 		lines.resize(processors);
 		for (int i = 0; i < processors; i++) {
 			lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
@@ -918,6 +928,8 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                 thisItersLookup.clear();
                 for (int i = 0; i < calcDists.size(); i++) {  calcDists[i].clear(); }
             }
+            
+            if (m->debug) {  m->mothurOut("[DEBUG]: iter = " + toString(thisIter) + ".\n"); }
 		}
         
 		if (m->debug) {  m->mothurOut("[DEBUG]: done with iters.\n"); }