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