chimeracheckcommand.cpp

   1 /*
   2  *  chimeracheckcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/31/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeracheckcommand.h"
  11 #include "chimeracheckrdp.h"
  12
  13 //***************************************************************************************************************
  14
  15 ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"fasta","processors","increment","template","ksize","svg", "name","outputdir","inputdir" };
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31                         map<string,string>::iterator it;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         //if the user changes the input directory command factory will send this info to us in the output parameter
  39                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  40                         if (inputDir == "not found"){   inputDir = "";          }
  41                         else {
  42                                 it = parameters.find("template");
  43                                 //user has given a template file
  44                                 if(it != parameters.end()){
  45                                         string path = hasPath(it->second);
  46                                         //if the user has not given a path then, add inputdir. else leave path alone.
  47                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  48                                 }
  49                         }
  50
  51                         //check for required parameters
  52                         fastafile = validParameter.validFile(parameters, "fasta", false);
  53                         if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
  54                         else {
  55                                 splitAtDash(fastafile, fastaFileNames);
  56
  57                                 //go through files and make sure they are good, if not, then disregard them
  58                                 for (int i = 0; i < fastaFileNames.size(); i++) {
  59                                         if (inputDir != "") {
  60                                                 string path = hasPath(fastaFileNames[i]);
  61                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  62                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
  63                                         }
  64
  65                                         int ableToOpen;
  66                                         ifstream in;
  67
  68                                         #ifdef USE_MPI
  69                                                 int pid;
  70                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
  71                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  72
  73                                                 if (pid == 0) {
  74                                         #endif
  75
  76                                         ableToOpen = openInputFile(fastaFileNames[i], in);
  77                                         in.close();
  78
  79                                         #ifdef USE_MPI
  80                                                         for (int j = 1; j < processors; j++) {
  81                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
  82                                                         }
  83                                                 }else{
  84                                                         MPI_Status status;
  85                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
  86                                                 }
  87
  88                                         #endif
  89
  90                                         if (ableToOpen == 1) {
  91                                                 m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
  92                                                 //erase from file list
  93                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
  94                                                 i--;
  95                                         }
  96                                 }
  97
  98                                 //make sure there is at least one valid file left
  99                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 100                         }
 101
 102                         //if the user changes the output directory command factory will send this info to us in the output parameter
 103                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 104
 105                         templatefile = validParameter.validFile(parameters, "template", true);
 106                         if (templatefile == "not open") { abort = true; }
 107                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("template is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
 108
 109                         namefile = validParameter.validFile(parameters, "name", false);
 110                         if (namefile == "not found") { namefile = ""; }
 111                         else {
 112                                 splitAtDash(namefile, nameFileNames);
 113
 114                                 //go through files and make sure they are good, if not, then disregard them
 115                                 for (int i = 0; i < nameFileNames.size(); i++) {
 116                                         if (inputDir != "") {
 117                                                 string path = hasPath(nameFileNames[i]);
 118                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 119                                                 if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 120                                         }
 121
 122                                         int ableToOpen;
 123                                         ifstream in;
 124
 125                                         #ifdef USE_MPI
 126                                                 int pid;
 127                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 128                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 129
 130                                                 if (pid == 0) {
 131                                         #endif
 132
 133                                         ableToOpen = openInputFile(nameFileNames[i], in);
 134                                         in.close();
 135
 136                                         #ifdef USE_MPI
 137                                                         for (int j = 1; j < processors; j++) {
 138                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
 139                                                         }
 140                                                 }else{
 141                                                         MPI_Status status;
 142                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 143                                                 }
 144
 145                                         #endif
 146
 147                                         if (ableToOpen == 1) {
 148                                                 m->mothurOut(nameFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
 149                                                 //erase from file list
 150                                                 nameFileNames.erase(nameFileNames.begin()+i);
 151                                                 i--;
 152                                         }
 153
 154                                 }
 155
 156                                 //make sure there is at least one valid file left
 157                                 if (nameFileNames.size() != 0) {
 158                                         if (nameFileNames.size() != fastaFileNames.size()) {
 159                                                  m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine();
 160                                                  abort = true;
 161                                         }
 162                                 }
 163                         }
 164
 165                         string temp = validParameter.validFile(parameters, "processors", false);                if (temp == "not found") { temp = "1"; }
 166                         convert(temp, processors);
 167
 168                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 169                         convert(temp, ksize);
 170
 171                         temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
 172                         svg = isTrue(temp);
 173                         if (nameFileNames.size() != 0) { svg = true; }
 174
 175                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
 176                         convert(temp, increment);
 177                 }
 178         }
 179         catch(exception& e) {
 180                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
 181                 exit(1);
 182         }
 183 }
 184 //**********************************************************************************************************************
 185
 186 void ChimeraCheckCommand::help(){
 187         try {
 188
 189                 m->mothurOut("The chimera.check command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 190                 m->mothurOut("This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n");
 191                 m->mothurOut("The chimera.check command parameters are fasta, template, processors, ksize, increment, svg and name.\n");
 192                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 193                 m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
 194                 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 195                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 196                 #ifdef USE_MPI
 197                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 198                 #endif
 199                 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n");
 200                 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7. \n");
 201                 m->mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n");
 202                 m->mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
 203                 m->mothurOut("You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n");
 204                 m->mothurOut("The chimera.check command should be in the following format: \n");
 205                 m->mothurOut("chimera.check(fasta=yourFastaFile, template=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n");
 206                 m->mothurOut("Example: chimera.check(fasta=AD.fasta, template=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n");
 207                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 208         }
 209         catch(exception& e) {
 210                 m->errorOut(e, "ChimeraCheckCommand", "help");
 211                 exit(1);
 212         }
 213 }
 214
 215 //***************************************************************************************************************
 216
 217 ChimeraCheckCommand::~ChimeraCheckCommand(){    /*      do nothing      */      }
 218
 219 //***************************************************************************************************************
 220
 221 int ChimeraCheckCommand::execute(){
 222         try{
 223
 224                 if (abort == true) { return 0; }
 225
 226                 for (int i = 0; i < fastaFileNames.size(); i++) {
 227
 228                         m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
 229
 230                         int start = time(NULL);
 231
 232                         string thisNameFile = "";
 233                         if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; }
 234
 235                         chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir);
 236
 237                         if (m->control_pressed) { delete chimera;       return 0;       }
 238
 239                         string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
 240                         outputNames.push_back(outputFileName);
 241
 242                 #ifdef USE_MPI
 243
 244                                 int pid, end, numSeqsPerProcessor;
 245                                 int tag = 2001;
 246                                 vector<long> MPIPos;
 247
 248                                 MPI_Status status;
 249                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 250                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 251
 252                                 MPI_File inMPI;
 253                                 MPI_File outMPI;
 254
 255                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 256                                 int inMode=MPI_MODE_RDONLY;
 257
 258                                 char outFilename[1024];
 259                                 strcpy(outFilename, outputFileName.c_str());
 260
 261                                 char inFileName[1024];
 262                                 strcpy(inFileName, fastaFileNames[i].c_str());
 263
 264                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 265                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 266
 267                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); } delete chimera; return 0;  }
 268
 269                                 if (pid == 0) { //you are the root process
 270                                         MPIPos = setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
 271
 272                                         //send file positions to all processes
 273                                         for(int j = 1; j < processors; j++) {
 274                                                 MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
 275                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, tag, MPI_COMM_WORLD);
 276                                         }
 277
 278                                         //figure out how many sequences you have to align
 279                                         numSeqsPerProcessor = numSeqs / processors;
 280                                         int startIndex =  pid * numSeqsPerProcessor;
 281                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 282
 283
 284                                         //align your part
 285                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 286
 287                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); }   delete chimera; return 0;  }
 288
 289                                         //wait on chidren
 290                                         for(int j = 1; j < processors; j++) {
 291                                                 char buf[4];
 292                                                 MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status);
 293                                         }
 294                                 }else{ //you are a child process
 295                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 296                                         MPIPos.resize(numSeqs+1);
 297                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 298
 299                                         //figure out how many sequences you have to align
 300                                         numSeqsPerProcessor = numSeqs / processors;
 301                                         int startIndex =  pid * numSeqsPerProcessor;
 302                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 303
 304                                         //align your part
 305                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 306
 307                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 308
 309                                         //tell parent you are done.
 310                                         char buf[4];
 311                                         strcpy(buf, "done");
 312                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 313                                 }
 314
 315                                 //close files
 316                                 MPI_File_close(&inMPI);
 317                                 MPI_File_close(&outMPI);
 318                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 319                 #else
 320
 321                         //break up file
 322                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 323                                 if(processors == 1){
 324                                         ifstream inFASTA;
 325                                         openInputFile(fastaFileNames[i], inFASTA);
 326                                         getNumSeqs(inFASTA, numSeqs);
 327                                         inFASTA.close();
 328
 329                                         lines.push_back(new linePair(0, numSeqs));
 330
 331                                         driver(lines[0], outputFileName, fastaFileNames[i]);
 332
 333                                         if (m->control_pressed) {
 334                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 335                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 336                                                 delete chimera;
 337                                                 return 0;
 338                                         }
 339
 340                                 }else{
 341                                         vector<int> positions;
 342                                         processIDS.resize(0);
 343
 344                                         ifstream inFASTA;
 345                                         openInputFile(fastaFileNames[i], inFASTA);
 346
 347                                         string input;
 348                                         while(!inFASTA.eof()){
 349                                                 input = getline(inFASTA);
 350                                                 if (input.length() != 0) {
 351                                                         if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 352                                                 }
 353                                         }
 354                                         inFASTA.close();
 355
 356                                         numSeqs = positions.size();
 357
 358                                         int numSeqsPerProcessor = numSeqs / processors;
 359
 360                                         for (int j = 0; j < processors; j++) {
 361                                                 long int startPos = positions[ j * numSeqsPerProcessor ];
 362                                                 if(j == processors - 1){
 363                                                         numSeqsPerProcessor = numSeqs - j * numSeqsPerProcessor;
 364                                                 }
 365                                                 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 366                                         }
 367
 368
 369                                         createProcesses(outputFileName, fastaFileNames[i]);
 370
 371                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 372
 373                                         //append output files
 374                                         for(int j=1;j<processors;j++){
 375                                                 appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
 376                                                 remove((outputFileName + toString(processIDS[j]) + ".temp").c_str());
 377                                         }
 378
 379                                         if (m->control_pressed) {
 380                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 381                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 382                                                 delete chimera;
 383                                                 return 0;
 384                                         }
 385                                 }
 386
 387                         #else
 388                                 ifstream inFASTA;
 389                                 openInputFile(fastaFileNames[i], inFASTA);
 390                                 getNumSeqs(inFASTA, numSeqs);
 391                                 inFASTA.close();
 392                                 lines.push_back(new linePair(0, numSeqs));
 393
 394                                 driver(lines[0], outputFileName, fastaFileNames[i]);
 395
 396                                 if (m->control_pressed) {
 397                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 398                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 399                                                 delete chimera;
 400                                                 return 0;
 401                                 }
 402                         #endif
 403                 #endif
 404                         delete chimera;
 405                         for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 406
 407                         m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine();
 408                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 409
 410                 }
 411
 412                 m->mothurOutEndLine();
 413                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 414                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 415                 m->mothurOutEndLine();
 416
 417                 return 0;
 418
 419         }
 420         catch(exception& e) {
 421                 m->errorOut(e, "ChimeraCheckCommand", "execute");
 422                 exit(1);
 423         }
 424 }
 425 //**********************************************************************************************************************
 426
 427 int ChimeraCheckCommand::driver(linePair* line, string outputFName, string filename){
 428         try {
 429                 ofstream out;
 430                 openOutputFile(outputFName, out);
 431
 432                 ofstream out2;
 433
 434                 ifstream inFASTA;
 435                 openInputFile(filename, inFASTA);
 436
 437                 inFASTA.seekg(line->start);
 438
 439                 for(int i=0;i<line->numSeqs;i++){
 440
 441                         if (m->control_pressed) {       return 1;       }
 442
 443                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 444
 445                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 446                                 //find chimeras
 447                                 chimera->getChimeras(candidateSeq);
 448
 449                                 if (m->control_pressed) {       delete candidateSeq; return 1;  }
 450
 451                                 //print results
 452                                 chimera->print(out, out2);
 453                         }
 454                         delete candidateSeq;
 455
 456                         //report progress
 457                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 458                 }
 459                 //report progress
 460                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 461
 462                 out.close();
 463                 inFASTA.close();
 464
 465                 return 0;
 466         }
 467         catch(exception& e) {
 468                 m->errorOut(e, "ChimeraCheckCommand", "driver");
 469                 exit(1);
 470         }
 471 }
 472 //**********************************************************************************************************************
 473 #ifdef USE_MPI
 474 int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos){
 475         try {
 476                 MPI_File outAccMPI;
 477                 MPI_Status status;
 478                 int pid;
 479                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 480
 481                 for(int i=0;i<num;i++){
 482
 483                         if (m->control_pressed) { return 0; }
 484
 485                         //read next sequence
 486                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 487
 488                         char* buf4 = new char[length];
 489                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 490
 491                         string tempBuf = buf4;
 492                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 493                         istringstream iss (tempBuf,istringstream::in);
 494                         delete buf4;
 495
 496                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 497
 498                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 499                                 //find chimeras
 500                                 chimera->getChimeras(candidateSeq);
 501
 502                                 //print results
 503                                 chimera->print(outMPI, outAccMPI);
 504                         }
 505                         delete candidateSeq;
 506
 507                         //report progress
 508                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 509                 }
 510                 //report progress
 511                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 512
 513                 return 0;
 514         }
 515         catch(exception& e) {
 516                 m->errorOut(e, "ChimeraCheckCommand", "driverMPI");
 517                 exit(1);
 518         }
 519 }
 520 #endif
 521
 522 /**************************************************************************************************/
 523
 524 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 525         try {
 526 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 527                 int process = 0;
 528                 //              processIDS.resize(0);
 529
 530                 //loop through and create all the processes you want
 531                 while (process != processors) {
 532                         int pid = fork();
 533
 534                         if (pid > 0) {
 535                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 536                                 process++;
 537                         }else if (pid == 0){
 538                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
 539                                 exit(0);
 540                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 541                 }
 542
 543                 //force parent to wait until all the processes are done
 544                 for (int i=0;i<processors;i++) {
 545                         int temp = processIDS[i];
 546                         wait(&temp);
 547                 }
 548
 549                 return 0;
 550 #endif
 551         }
 552         catch(exception& e) {
 553                 m->errorOut(e, "ChimeraCheckCommand", "createProcesses");
 554                 exit(1);
 555         }
 556 }
 557 /**************************************************************************************************/
 558
 559