fixed bug with blastdb.cpp

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 0e7e19bbda16ff8f4222562c0ffe95f78b335d35..fed36135db3116567dea8b323f9ec0803cd29da8 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -509,6 +509,16 @@ int ChimeraSlayerCommand::execute(){
                                        //do your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
                                        
+                                       int numNoParents = chimera->getNumNoParents();
+                                       int temp;
+                                       for(int i = 1; i < processors; i++) { 
+                                               MPI_Recv(&temp, 1, MPI_INT, 1, tag, MPI_COMM_WORLD, &status);
+                                               numNoParents += temp;
+                                       }
+                                       
+                                       
+                                       if (numSeqs == numNoParents) {  m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+                                       
                                        if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  delete chimera; return 0;  }
 
                                }else{ //you are a child process
@@ -524,6 +534,9 @@ int ChimeraSlayerCommand::execute(){
                                        
                                                //do your part
                                                driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
+                                               
+                                               int numNoParents = chimera->getNumNoParents();
+                                               MPI_Send(&numNoParents, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
                                        
                                                if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
                                
@@ -556,6 +569,9 @@ int ChimeraSlayerCommand::execute(){
                                if(processors == 1){
                                        numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
                                        
+                                       int numNoParents = chimera->getNumNoParents();
+                                       if (numNoParents == numSeqs) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+                                       
                                        if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {      remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
                                        
                                }else{
@@ -592,6 +608,10 @@ int ChimeraSlayerCommand::execute(){
                        #else
                                numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
                                
+                               int numNoParents = chimera->getNumNoParents();
+                               if (numNoParents == numSeqs) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+
+                               
                                if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {      remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
                                
                        #endif
@@ -670,7 +690,6 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f
                        string candidateAligned = candidateSeq->getAligned();
                        
                        if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
-                               
                                if (candidateSeq->getAligned().length() != templateSeqsLength) {  
                                        m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
                                }else{
@@ -906,9 +925,8 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                                ofstream out;
                                string tempFile = outputFileName + toString(getpid()) + ".num.temp";
                                m->openOutputFile(tempFile, out);
-                               out << num << endl;
+                               out << num << '\t' << chimera->getNumNoParents() << endl;
                                out.close();
-                               
                                exit(0);
                        }else { 
                                m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
@@ -923,14 +941,17 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                        wait(&temp);
                }
                
+               int numNoParents = 0;
                for (int i = 0; i < processIDS.size(); i++) {
                        ifstream in;
                        string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
                        m->openInputFile(tempFile, in);
-                       if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+                       if (!in.eof()) { int tempNum = 0; int tempNumParents = 0; in >> tempNum >> tempNumParents; num += tempNum; numNoParents += tempNumParents; }
                        in.close(); remove(tempFile.c_str());
                }
                
+               if (num == numNoParents) {  m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
+               
                return num;
 #endif         
        }