X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;h=3d3c9aea99401c492676e210173d7b397e205a70;hb=0c78e45408d8c099bc51579225ebfc227f7523b2;hp=280fd8f0acf60c045f732ac07172476c7f9ab29e;hpb=cd985cf388dcc4c7de8251339206aec5f7e12f1e;p=mothur.git diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp index 280fd8f..3d3c9ae 100644 --- a/chimeraccodecommand.cpp +++ b/chimeraccodecommand.cpp @@ -40,14 +40,6 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { if (inputDir == "not found"){ inputDir = ""; } else { string path; - it = parameters.find("fasta"); - //user has given a template file - if(it != parameters.end()){ - path = hasPath(it->second); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["fasta"] = inputDir + it->second; } - } - it = parameters.find("template"); //user has given a template file if(it != parameters.end()){ @@ -57,11 +49,56 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option) { } } - //check for required parameters - fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; } + fastafile = validParameter.validFile(parameters, "fasta", false); + if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.ccode command."); m->mothurOutEndLine(); abort = true; } + else { + splitAtDash(fastafile, fastaFileNames); + + //go through files and make sure they are good, if not, then disregard them + for (int i = 0; i < fastaFileNames.size(); i++) { + if (inputDir != "") { + string path = hasPath(fastaFileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; } + } + + int ableToOpen; + ifstream in; + + #ifdef USE_MPI + int pid; + MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + if (pid == 0) { + #endif + + ableToOpen = openInputFile(fastaFileNames[i], in); + in.close(); + + #ifdef USE_MPI + for (int j = 1; j < processors; j++) { + MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); + } + }else{ + MPI_Status status; + MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + } + + #endif + + if (ableToOpen == 1) { + m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; + } + } + + //make sure there is at least one valid file left + if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; } + } //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ @@ -117,6 +154,7 @@ void ChimeraCcodeCommand::help(){ m->mothurOut("This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n"); m->mothurOut("The chimera.ccode command parameters are fasta, template, filter, mask, processors, window and numwanted.\n"); m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n"); + m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n"); m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n"); m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"); @@ -128,7 +166,7 @@ void ChimeraCcodeCommand::help(){ m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n"); m->mothurOut("The chimera.ccode command should be in the following format: \n"); m->mothurOut("chimera.ccode(fasta=yourFastaFile, template=yourTemplate) \n"); - m->mothurOut("Example: chimera.seqs(fasta=AD.align, template=core_set_aligned.imputed.fasta) \n"); + m->mothurOut("Example: chimera.ccode(fasta=AD.align, template=core_set_aligned.imputed.fasta) \n"); m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); } catch(exception& e) { @@ -148,293 +186,250 @@ int ChimeraCcodeCommand::execute(){ if (abort == true) { return 0; } - int start = time(NULL); - - //set user options - if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); } - - chimera = new Ccode(fastafile, templatefile, filter, maskfile, window, numwanted, outputDir); - - //is your template aligned? - if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; } - templateSeqsLength = chimera->getLength(); - - string outputFileName, accnosFileName; - if (maskfile != "") { - outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".ccode.chimeras"; - accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".ccode.accnos"; - }else { - outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "ccode.chimeras"; - accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + "ccode.accnos"; - } - - string mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo"; - bool hasAccnos = true; - - if (m->control_pressed) { delete chimera; return 0; } + for (int s = 0; s < fastaFileNames.size(); s++) { + + m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine(); - #ifdef USE_MPI - - int pid, end, numSeqsPerProcessor; - int tag = 2001; - vector MPIPos; - MPIWroteAccnos = false; - - MPI_Status status; - MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are - MPI_Comm_size(MPI_COMM_WORLD, &processors); - - MPI_File inMPI; - MPI_File outMPI; - MPI_File outMPIAccnos; + int start = time(NULL); - int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; - int inMode=MPI_MODE_RDONLY; + //set user options + if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine(); } - //char* outFilename = new char[outputFileName.length()]; - //memcpy(outFilename, outputFileName.c_str(), outputFileName.length()); - - char outFilename[1024]; - strcpy(outFilename, outputFileName.c_str()); + chimera = new Ccode(fastaFileNames[s], templatefile, filter, maskfile, window, numwanted, outputDir); - //char* outAccnosFilename = new char[accnosFileName.length()]; - //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length()); + //is your template aligned? + if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; } + templateSeqsLength = chimera->getLength(); - char outAccnosFilename[1024]; - strcpy(outAccnosFilename, accnosFileName.c_str()); + string outputFileName, accnosFileName; + if (maskfile != "") { + outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras"; + accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos"; + }else { + outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ccode.chimeras"; + accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ccode.accnos"; + } - //char* inFileName = new char[fastafile.length()]; - //memcpy(inFileName, fastafile.c_str(), fastafile.length()); + string mapInfo = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "mapinfo"; - char inFileName[1024]; - strcpy(inFileName, fastafile.c_str()); - - MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer - MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI); - MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos); + if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; } - //delete inFileName; - //delete outFilename; - //delete outAccnosFilename; - - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; } + #ifdef USE_MPI - if (pid == 0) { //you are the root process - string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n"; - - //print header - int length = outTemp.length(); - char* buf2 = new char[length]; - memcpy(buf2, outTemp.c_str(), length); - - MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status); - delete buf2; + int pid, end, numSeqsPerProcessor; + int tag = 2001; + vector MPIPos; + + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + MPI_Comm_size(MPI_COMM_WORLD, &processors); - MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs + MPI_File inMPI; + MPI_File outMPI; + MPI_File outMPIAccnos; - //send file positions to all processes - for(int i = 1; i < processors; i++) { - MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); - MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); - } + int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; + int inMode=MPI_MODE_RDONLY; - //figure out how many sequences you have to align - numSeqsPerProcessor = numSeqs / processors; - int startIndex = pid * numSeqsPerProcessor; - if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + char outFilename[1024]; + strcpy(outFilename, outputFileName.c_str()); + char outAccnosFilename[1024]; + strcpy(outAccnosFilename, accnosFileName.c_str()); + + char inFileName[1024]; + strcpy(inFileName, fastaFileNames[s].c_str()); + + MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer + MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI); + MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } - //align your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); + if (pid == 0) { //you are the root process + string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n"; + + //print header + int length = outTemp.length(); + char* buf2 = new char[length]; + memcpy(buf2, outTemp.c_str(), length); + + MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status); + delete buf2; + + MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs + + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } + + //figure out how many sequences you have to align + numSeqsPerProcessor = numSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; } + //align your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } - for (int i = 1; i < processors; i++) { - bool tempResult; - MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status); - if (tempResult != 0) { MPIWroteAccnos = true; } + }else{ //you are a child process + MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + MPIPos.resize(numSeqs+1); + MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + + //figure out how many sequences you have to align + numSeqsPerProcessor = numSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + + + //align your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } } - }else{ //you are a child process - MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); - MPIPos.resize(numSeqs+1); - MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); - - //figure out how many sequences you have to align - numSeqsPerProcessor = numSeqs / processors; - int startIndex = pid * numSeqsPerProcessor; - if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } + //close files + MPI_File_close(&inMPI); + MPI_File_close(&outMPI); + MPI_File_close(&outMPIAccnos); - //align your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos); - - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); delete chimera; return 0; } - - MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); - } - - //close files - MPI_File_close(&inMPI); - MPI_File_close(&outMPI); - MPI_File_close(&outMPIAccnos); + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + + #else + ofstream outHeader; + string tempHeader = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + maskfile + "ccode.chimeras.tempHeader"; + openOutputFile(tempHeader, outHeader); - MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + outHeader << "For full window mapping info refer to " << mapInfo << endl << endl; + + outHeader.close(); - //delete accnos file if blank - if (pid == 0) { - if (!MPIWroteAccnos) { - //MPI_Info info; - //MPI_File_delete(outAccnosFilename, info); - hasAccnos = false; - remove(accnosFileName.c_str()); + //break up file + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if(processors == 1){ + ifstream inFASTA; + openInputFile(fastaFileNames[s], inFASTA); + getNumSeqs(inFASTA, numSeqs); + inFASTA.close(); + + lines.push_back(new linePair(0, numSeqs)); + + driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); + + if (m->control_pressed) { + 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{ + vector positions; + processIDS.resize(0); + + ifstream inFASTA; + openInputFile(fastaFileNames[s], inFASTA); + + string input; + while(!inFASTA.eof()){ + input = getline(inFASTA); + if (input.length() != 0) { + if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + } + } + inFASTA.close(); + + numSeqs = positions.size(); + + int numSeqsPerProcessor = numSeqs / processors; + + for (int i = 0; i < processors; i++) { + long int startPos = positions[ i * numSeqsPerProcessor ]; + if(i == processors - 1){ + numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; + } + lines.push_back(new linePair(startPos, numSeqsPerProcessor)); + } + + + createProcesses(outputFileName, fastaFileNames[s], accnosFileName); + + rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); + rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str()); + + //append output files + for(int i=1;icontrol_pressed) { + remove(outputFileName.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 - ofstream outHeader; - string tempHeader = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + "ccode.chimeras.tempHeader"; - openOutputFile(tempHeader, outHeader); - - outHeader << "For full window mapping info refer to " << mapInfo << endl << endl; - outHeader.close(); - - //break up file - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - if(processors == 1){ + #else ifstream inFASTA; - openInputFile(fastafile, inFASTA); + openInputFile(fastaFileNames[s], inFASTA); getNumSeqs(inFASTA, numSeqs); inFASTA.close(); - lines.push_back(new linePair(0, numSeqs)); - driver(lines[0], outputFileName, fastafile, accnosFileName); + driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName); if (m->control_pressed) { - remove(outputFileName.c_str()); - remove(tempHeader.c_str()); - remove(accnosFileName.c_str()); - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - delete chimera; - return 0; - } - - //delete accnos file if its blank - if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } - - }else{ - vector positions; - processIDS.resize(0); - - ifstream inFASTA; - openInputFile(fastafile, inFASTA); - - string input; - while(!inFASTA.eof()){ - input = getline(inFASTA); - if (input.length() != 0) { - if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } - } - } - inFASTA.close(); - - numSeqs = positions.size(); - - int numSeqsPerProcessor = numSeqs / processors; - - for (int i = 0; i < processors; i++) { - long int startPos = positions[ i * numSeqsPerProcessor ]; - if(i == processors - 1){ - numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; - } - lines.push_back(new linePair(startPos, numSeqsPerProcessor)); - } - - - createProcesses(outputFileName, fastafile, accnosFileName); - - rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); - - //append output files - for(int i=1;i nonBlankAccnosFiles; - //delete blank accnos files generated with multiple processes - for(int i=0;icontrol_pressed) { - remove(outputFileName.c_str()); - remove(accnosFileName.c_str()); - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - delete chimera; - return 0; - } - - } - - #else - ifstream inFASTA; - openInputFile(fastafile, inFASTA); - getNumSeqs(inFASTA, numSeqs); - inFASTA.close(); - lines.push_back(new linePair(0, numSeqs)); + #endif + + appendFiles(outputFileName, tempHeader); + + remove(outputFileName.c_str()); + rename(tempHeader.c_str(), outputFileName.c_str()); + #endif + + delete chimera; - driver(lines[0], outputFileName, fastafile, accnosFileName); + outputNames.push_back(outputFileName); + outputNames.push_back(mapInfo); + outputNames.push_back(accnosFileName); - if (m->control_pressed) { - remove(outputFileName.c_str()); - remove(tempHeader.c_str()); - remove(accnosFileName.c_str()); - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - delete chimera; - return 0; - } + for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - //delete accnos file if its blank - if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } - #endif - - //m->mothurOut("Output File Names: "); - //if ((filter) && (method == "bellerophon")) { m->mothurOut( - //if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; } - // else { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; } - - appendFiles(outputFileName, tempHeader); - - remove(outputFileName.c_str()); - rename(tempHeader.c_str(), outputFileName.c_str()); - #endif - - delete chimera; - + m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); + } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - m->mothurOut(outputFileName); m->mothurOutEndLine(); - if (hasAccnos) { m->mothurOut(accnosFileName); m->mothurOutEndLine(); } + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); - - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - - m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); return 0; @@ -537,7 +532,6 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File //print results bool isChimeric = chimera->print(outMPI, outAccMPI); - if (isChimeric) { MPIWroteAccnos = true; } } } delete candidateSeq;