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
  12 //***************************************************************************************************************
  13
  14 ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
  15         try {
  16                 abort = false;
  17
  18                 //allow user to run help
  19                 if(option == "help") { help(); abort = true; }
  20
  21                 else {
  22                         //valid paramters for this command
  23                         string Array[] =  {"fasta","processors","increment","template","ksize","svg", "name","outputdir","inputdir" };
  24                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  25
  26                         OptionParser parser(option);
  27                         map<string,string> parameters = parser.getParameters();
  28
  29                         ValidParameters validParameter;
  30                         map<string,string>::iterator it;
  31
  32                         //check to make sure all parameters are valid for command
  33                         for (it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         //if the user changes the input directory command factory will send this info to us in the output parameter
  38                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  39                         if (inputDir == "not found"){   inputDir = "";          }
  40                         else {
  41                                 it = parameters.find("template");
  42                                 //user has given a template file
  43                                 if(it != parameters.end()){
  44                                         string path = hasPath(it->second);
  45                                         //if the user has not given a path then, add inputdir. else leave path alone.
  46                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  47                                 }
  48                         }
  49
  50                         //check for required parameters
  51                         fastafile = validParameter.validFile(parameters, "fasta", false);
  52                         if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
  53                         else {
  54                                 splitAtDash(fastafile, fastaFileNames);
  55
  56                                 //go through files and make sure they are good, if not, then disregard them
  57                                 for (int i = 0; i < fastaFileNames.size(); i++) {
  58                                         if (inputDir != "") {
  59                                                 string path = hasPath(fastaFileNames[i]);
  60                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  61                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
  62                                         }
  63
  64                                         int ableToOpen;
  65                                         ifstream in;
  66
  67                                         #ifdef USE_MPI
  68                                                 int pid;
  69                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
  70                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  71
  72                                                 if (pid == 0) {
  73                                         #endif
  74
  75                                         ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
  76
  77                                         //if you can't open it, try default location
  78                                         if (ableToOpen == 1) {
  79                                                 if (m->getDefaultPath() != "") { //default path is set
  80                                                         string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
  81                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
  82                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
  83                                                         fastaFileNames[i] = tryPath;
  84                                                 }
  85                                         }
  86                                         in.close();
  87
  88                                         #ifdef USE_MPI
  89                                                         for (int j = 1; j < processors; j++) {
  90                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
  91                                                         }
  92                                                 }else{
  93                                                         MPI_Status status;
  94                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
  95                                                 }
  96
  97                                         #endif
  98
  99                                         if (ableToOpen == 1) {
 100                                                 m->mothurOut("Unable to open " + fastaFileNames[i] +". It will be disregarded."); m->mothurOutEndLine();
 101                                                 //erase from file list
 102                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 103                                                 i--;
 104                                         }
 105                                 }
 106
 107                                 //make sure there is at least one valid file left
 108                                 if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 109                         }
 110
 111                         //if the user changes the output directory command factory will send this info to us in the output parameter
 112                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 113
 114                         templatefile = validParameter.validFile(parameters, "template", true);
 115                         if (templatefile == "not open") { abort = true; }
 116                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("template is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true;  }
 117
 118                         namefile = validParameter.validFile(parameters, "name", false);
 119                         if (namefile == "not found") { namefile = ""; }
 120                         else {
 121                                 splitAtDash(namefile, nameFileNames);
 122
 123                                 //go through files and make sure they are good, if not, then disregard them
 124                                 for (int i = 0; i < nameFileNames.size(); i++) {
 125                                         if (inputDir != "") {
 126                                                 string path = hasPath(nameFileNames[i]);
 127                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 128                                                 if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 129                                         }
 130
 131                                         int ableToOpen;
 132                                         ifstream in;
 133
 134                                         #ifdef USE_MPI
 135                                                 int pid;
 136                                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 137                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 138
 139                                                 if (pid == 0) {
 140                                         #endif
 141
 142                                         ableToOpen = openInputFile(nameFileNames[i], in, "noerror");
 143
 144                                         //if you can't open it, try default location
 145                                         if (ableToOpen == 1) {
 146                                                 if (m->getDefaultPath() != "") { //default path is set
 147                                                         string tryPath = m->getDefaultPath() + getSimpleName(nameFileNames[i]);
 148                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 149                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
 150                                                         nameFileNames[i] = tryPath;
 151                                                 }
 152                                         }
 153                                         in.close();
 154
 155                                         #ifdef USE_MPI
 156                                                         for (int j = 1; j < processors; j++) {
 157                                                                 MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
 158                                                         }
 159                                                 }else{
 160                                                         MPI_Status status;
 161                                                         MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 162                                                 }
 163
 164                                         #endif
 165
 166                                         if (ableToOpen == 1) {
 167                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 168                                                 //erase from file list
 169                                                 nameFileNames.erase(nameFileNames.begin()+i);
 170                                                 i--;
 171                                         }
 172
 173                                 }
 174
 175                                 //make sure there is at least one valid file left
 176                                 if (nameFileNames.size() != 0) {
 177                                         if (nameFileNames.size() != fastaFileNames.size()) {
 178                                                  m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine();
 179                                                  abort = true;
 180                                         }
 181                                 }
 182                         }
 183
 184                         string temp = validParameter.validFile(parameters, "processors", false);                if (temp == "not found") { temp = "1"; }
 185                         convert(temp, processors);
 186
 187                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 188                         convert(temp, ksize);
 189
 190                         temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
 191                         svg = isTrue(temp);
 192                         if (nameFileNames.size() != 0) { svg = true; }
 193
 194                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
 195                         convert(temp, increment);
 196                 }
 197         }
 198         catch(exception& e) {
 199                 m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
 200                 exit(1);
 201         }
 202 }
 203 //**********************************************************************************************************************
 204
 205 void ChimeraCheckCommand::help(){
 206         try {
 207
 208                 m->mothurOut("The chimera.check command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 209                 m->mothurOut("This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n");
 210                 m->mothurOut("The chimera.check command parameters are fasta, template, processors, ksize, increment, svg and name.\n");
 211                 m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 212                 m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
 213                 m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 214                 m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 215                 #ifdef USE_MPI
 216                 m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 217                 #endif
 218                 m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 10.\n");
 219                 m->mothurOut("The ksize parameter allows you to input kmersize, default is 7. \n");
 220                 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");
 221                 m->mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
 222                 m->mothurOut("You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n");
 223                 m->mothurOut("The chimera.check command should be in the following format: \n");
 224                 m->mothurOut("chimera.check(fasta=yourFastaFile, template=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n");
 225                 m->mothurOut("Example: chimera.check(fasta=AD.fasta, template=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n");
 226                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 227         }
 228         catch(exception& e) {
 229                 m->errorOut(e, "ChimeraCheckCommand", "help");
 230                 exit(1);
 231         }
 232 }
 233
 234 //***************************************************************************************************************
 235
 236 ChimeraCheckCommand::~ChimeraCheckCommand(){    /*      do nothing      */      }
 237
 238 //***************************************************************************************************************
 239
 240 int ChimeraCheckCommand::execute(){
 241         try{
 242
 243                 if (abort == true) { return 0; }
 244
 245                 for (int i = 0; i < fastaFileNames.size(); i++) {
 246
 247                         m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
 248
 249                         int start = time(NULL);
 250
 251                         string thisNameFile = "";
 252                         if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; }
 253
 254                         chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir);
 255
 256                         if (m->control_pressed) { delete chimera;       return 0;       }
 257
 258                         string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
 259                         outputNames.push_back(outputFileName);
 260
 261                 #ifdef USE_MPI
 262
 263                                 int pid, end, numSeqsPerProcessor;
 264                                 int tag = 2001;
 265                                 vector<long> MPIPos;
 266
 267                                 MPI_Status status;
 268                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 269                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 270
 271                                 MPI_File inMPI;
 272                                 MPI_File outMPI;
 273
 274                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 275                                 int inMode=MPI_MODE_RDONLY;
 276
 277                                 char outFilename[1024];
 278                                 strcpy(outFilename, outputFileName.c_str());
 279
 280                                 char inFileName[1024];
 281                                 strcpy(inFileName, fastaFileNames[i].c_str());
 282
 283                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 284                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 285
 286                                 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;  }
 287
 288                                 if (pid == 0) { //you are the root process
 289                                         MPIPos = setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
 290
 291                                         //send file positions to all processes
 292                                         for(int j = 1; j < processors; j++) {
 293                                                 MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
 294                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, tag, MPI_COMM_WORLD);
 295                                         }
 296
 297                                         //figure out how many sequences you have to align
 298                                         numSeqsPerProcessor = numSeqs / processors;
 299                                         int startIndex =  pid * numSeqsPerProcessor;
 300                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 301
 302
 303                                         //align your part
 304                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 305
 306                                         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;  }
 307
 308                                         //wait on chidren
 309                                         for(int j = 1; j < processors; j++) {
 310                                                 char buf[4];
 311                                                 MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status);
 312                                         }
 313                                 }else{ //you are a child process
 314                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 315                                         MPIPos.resize(numSeqs+1);
 316                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 317
 318                                         //figure out how many sequences you have to align
 319                                         numSeqsPerProcessor = numSeqs / processors;
 320                                         int startIndex =  pid * numSeqsPerProcessor;
 321                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 322
 323                                         //align your part
 324                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 325
 326                                         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;  }
 327
 328                                         //tell parent you are done.
 329                                         char buf[4];
 330                                         strcpy(buf, "done");
 331                                         MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 332                                 }
 333
 334                                 //close files
 335                                 MPI_File_close(&inMPI);
 336                                 MPI_File_close(&outMPI);
 337                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 338                 #else
 339
 340                         //break up file
 341                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 342                                 if(processors == 1){
 343                                         ifstream inFASTA;
 344                                         openInputFile(fastaFileNames[i], inFASTA);
 345                                         getNumSeqs(inFASTA, numSeqs);
 346                                         inFASTA.close();
 347
 348                                         lines.push_back(new linePair(0, numSeqs));
 349
 350                                         driver(lines[0], outputFileName, fastaFileNames[i]);
 351
 352                                         if (m->control_pressed) {
 353                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 354                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 355                                                 delete chimera;
 356                                                 return 0;
 357                                         }
 358
 359                                 }else{
 360                                         vector<unsigned long int> positions;
 361                                         processIDS.resize(0);
 362
 363                                         ifstream inFASTA;
 364                                         openInputFile(fastaFileNames[i], inFASTA);
 365
 366                                         string input;
 367                                         while(!inFASTA.eof()){
 368                                                 input = getline(inFASTA);
 369                                                 if (input.length() != 0) {
 370                                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 371                                                 }
 372                                         }
 373                                         inFASTA.close();
 374
 375                                         numSeqs = positions.size();
 376
 377                                         int numSeqsPerProcessor = numSeqs / processors;
 378
 379                                         for (int j = 0; j < processors; j++) {
 380                                                 unsigned long int startPos = positions[ j * numSeqsPerProcessor ];
 381                                                 if(j == processors - 1){
 382                                                         numSeqsPerProcessor = numSeqs - j * numSeqsPerProcessor;
 383                                                 }
 384                                                 lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 385                                         }
 386
 387
 388                                         createProcesses(outputFileName, fastaFileNames[i]);
 389
 390                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 391
 392                                         //append output files
 393                                         for(int j=1;j<processors;j++){
 394                                                 appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
 395                                                 remove((outputFileName + toString(processIDS[j]) + ".temp").c_str());
 396                                         }
 397
 398                                         if (m->control_pressed) {
 399                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 400                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 401                                                 delete chimera;
 402                                                 return 0;
 403                                         }
 404                                 }
 405
 406                         #else
 407                                 ifstream inFASTA;
 408                                 openInputFile(fastaFileNames[i], inFASTA);
 409                                 getNumSeqs(inFASTA, numSeqs);
 410                                 inFASTA.close();
 411                                 lines.push_back(new linePair(0, numSeqs));
 412
 413                                 driver(lines[0], outputFileName, fastaFileNames[i]);
 414
 415                                 if (m->control_pressed) {
 416                                                 for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 417                                                 for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); }
 418                                                 delete chimera;
 419                                                 return 0;
 420                                 }
 421                         #endif
 422                 #endif
 423                         delete chimera;
 424                         for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
 425
 426                         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();
 427                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 428
 429                 }
 430
 431                 m->mothurOutEndLine();
 432                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 433                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 434                 m->mothurOutEndLine();
 435
 436                 return 0;
 437
 438         }
 439         catch(exception& e) {
 440                 m->errorOut(e, "ChimeraCheckCommand", "execute");
 441                 exit(1);
 442         }
 443 }
 444 //**********************************************************************************************************************
 445
 446 int ChimeraCheckCommand::driver(linePair* line, string outputFName, string filename){
 447         try {
 448                 ofstream out;
 449                 openOutputFile(outputFName, out);
 450
 451                 ofstream out2;
 452
 453                 ifstream inFASTA;
 454                 openInputFile(filename, inFASTA);
 455
 456                 inFASTA.seekg(line->start);
 457
 458                 for(int i=0;i<line->numSeqs;i++){
 459
 460                         if (m->control_pressed) {       return 1;       }
 461
 462                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 463
 464                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 465                                 //find chimeras
 466                                 chimera->getChimeras(candidateSeq);
 467
 468                                 if (m->control_pressed) {       delete candidateSeq; return 1;  }
 469
 470                                 //print results
 471                                 chimera->print(out, out2);
 472                         }
 473                         delete candidateSeq;
 474
 475                         //report progress
 476                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1)); m->mothurOutEndLine();           }
 477                 }
 478                 //report progress
 479                 if((line->numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(line->numSeqs)); m->mothurOutEndLine();         }
 480
 481                 out.close();
 482                 inFASTA.close();
 483
 484                 return 0;
 485         }
 486         catch(exception& e) {
 487                 m->errorOut(e, "ChimeraCheckCommand", "driver");
 488                 exit(1);
 489         }
 490 }
 491 //**********************************************************************************************************************
 492 #ifdef USE_MPI
 493 int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos){
 494         try {
 495                 MPI_File outAccMPI;
 496                 MPI_Status status;
 497                 int pid;
 498                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 499
 500                 for(int i=0;i<num;i++){
 501
 502                         if (m->control_pressed) { return 0; }
 503
 504                         //read next sequence
 505                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 506
 507                         char* buf4 = new char[length];
 508                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 509
 510                         string tempBuf = buf4;
 511                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 512                         istringstream iss (tempBuf,istringstream::in);
 513                         delete buf4;
 514
 515                         Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
 516
 517                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 518                                 //find chimeras
 519                                 chimera->getChimeras(candidateSeq);
 520
 521                                 //print results
 522                                 chimera->print(outMPI, outAccMPI);
 523                         }
 524                         delete candidateSeq;
 525
 526                         //report progress
 527                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 528                 }
 529                 //report progress
 530                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 531
 532                 return 0;
 533         }
 534         catch(exception& e) {
 535                 m->errorOut(e, "ChimeraCheckCommand", "driverMPI");
 536                 exit(1);
 537         }
 538 }
 539 #endif
 540
 541 /**************************************************************************************************/
 542
 543 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 544         try {
 545 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 546                 int process = 0;
 547                 //              processIDS.resize(0);
 548
 549                 //loop through and create all the processes you want
 550                 while (process != processors) {
 551                         int pid = fork();
 552
 553                         if (pid > 0) {
 554                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 555                                 process++;
 556                         }else if (pid == 0){
 557                                 driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
 558                                 exit(0);
 559                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 560                 }
 561
 562                 //force parent to wait until all the processes are done
 563                 for (int i=0;i<processors;i++) {
 564                         int temp = processIDS[i];
 565                         wait(&temp);
 566                 }
 567
 568                 return 0;
 569 #endif
 570         }
 571         catch(exception& e) {
 572                 m->errorOut(e, "ChimeraCheckCommand", "createProcesses");
 573                 exit(1);
 574         }
 575 }
 576 /**************************************************************************************************/
 577
 578