int main(int argc, char *argv[]) {
if (!Fastq2FastaOptions::parseOpts(argc, argv)) exit(1);
Cleanup::prepare();
OptionsBaseInterface::FileListType &inputs = Options::getOptions().getInputFiles();
long splitSizeBase = Fastq2FastaOptions::getOptions().getSplitSizeMegaBase() * 1000000;
ReadSet reads;
LOG_VERBOSE(1, "Reading Input Files" );
reads.appendAllFiles(inputs);
LOG_VERBOSE(1, "loaded " << reads.getSize() << " Reads, " << reads.getBaseCount()
<< " Bases ");
reads.identifyPairs();
long currentBase = 0;
OfstreamMap ofmap;
string outputFilename = Options::getOptions().getOutputFile();
bool hasOfMap = false;
ostream *out = &cout;
int partitionNum = 1;
if (!outputFilename.empty()) {
ofmap = OfstreamMap(outputFilename);
hasOfMap = true;
} else {
splitSizeBase = 0; // do not support splitting when no output is specified
}
bool splitPairs = Fastq2FastaOptions::getOptions().getSplitPairs() != 0;
string filekey;
for(ReadSet::ReadSetSizeType pairIdx = 0 ; pairIdx < reads.getPairSize(); pairIdx++) {
ReadSet::Pair pair = reads.getPair(pairIdx);
ReadSet::ReadSetSizeType lesserIdx = std::min(pair.read1, pair.read2);
if (hasOfMap) {
filekey = reads.getReadFileNamePrefix(lesserIdx);
} else {
filekey.clear();
}
if (splitSizeBase > 0) {
SequenceLengthType len = reads.getRead(lesserIdx).getLength();
currentBase += len;
if (currentBase > splitSizeBase) {
// new output handle
partitionNum++;
currentBase = len;
}
filekey += "-" + boost::lexical_cast<string>( partitionNum );
}
if (reads.isValidRead(pair.read1) && reads.isValidRead(pair.read2)) {
const Read read = reads.getRead(pair.read1);
if (hasOfMap) {
if (splitPairs) {
filekey += "-1";
}
out = &( ofmap.getOfstream(filekey) );
}
reads.getRead(pair.read1).write(*out);
if (splitPairs) {
filekey[filekey.length()-1] = '2';
out = &( ofmap.getOfstream(filekey) );
}
reads.getRead(pair.read2).write(*out);
} else {
if (hasOfMap) {
out = &( ofmap.getOfstream(filekey) );
}
reads.getRead(lesserIdx).write(*out);
}
}
}
int main(int argc, char *argv[]) {
ForkDaemon::initialize();
ScopedMPIComm< DistributedNucleatingAssemblerOptions > world(argc, argv);
Cleanup::prepare();
try {
double timing1, timing2;
timing1 = MPI_Wtime();
OptionsBaseInterface::FileListType &inputFiles =
Options::getOptions().getInputFiles();
std::string contigFile =
ContigExtenderBaseOptions::getOptions().getContigFile();
std::string finalContigFile;
double minimumCoverage =
ContigExtenderBaseOptions::getOptions().getMinimumCoverage();
long maxIterations =
DistributedNucleatingAssemblerOptions::getOptions().getMaxIterations();
ReadSet reads;
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Reading Input Files" );
reads.appendAllFiles(inputFiles, world.rank(), world.size());
reads.identifyPairs();
setGlobalReadSetConstants(world, reads);
timing2 = MPI_Wtime();
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "loaded " << reads.getGlobalSize() << " Reads, (local:" << reads.getSize() << " pair:" << reads.getPairSize() << ") in " << (timing2-timing1) << " seconds" );
LOG_DEBUG_GATHER(1, MemoryUtils::getMemoryUsage());
if (FilterKnownOdditiesOptions::getOptions().getSkipArtifactFilter() == 0) {
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Preparing artifact filter: ");
FilterKnownOddities filter;
LOG_VERBOSE_OPTIONAL(2, world.rank() == 0, "Applying sequence artifact filter to Input Files");
unsigned long filtered = filter.applyFilter(reads);
LOG_VERBOSE_GATHER(2, "local filter affected (trimmed/removed) " << filtered << " Reads ");
LOG_DEBUG_GATHER(1, MemoryUtils::getMemoryUsage());
unsigned long allFiltered;
mpi::reduce(world, filtered, allFiltered, std::plus<unsigned long>(), 0);
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "distributed filter (trimmed/removed) " << allFiltered << " Reads.");
}
boost::shared_ptr< MatcherInterface > matcher;
if (KmerBaseOptions::getOptions().getKmerSize() == 0) {
matcher.reset( new Vmatch(world, UniqueName::generateHashName(inputFiles), reads) );
} else {
matcher.reset( new KmerMatch(world, reads) );
}
SequenceLengthType minKmerSize, maxKmerSize, kmerStep, maxExtend;
ContigExtender<KS>::getMinMaxKmerSize(reads, minKmerSize, maxKmerSize,
kmerStep);
maxKmerSize = boost::mpi::all_reduce(world, maxKmerSize, mpi::minimum<
SequenceLengthType>());
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Kmer size ranges: " << minKmerSize << "\t" << maxKmerSize << "\t" << kmerStep);
maxExtend = maxKmerSize;
timing1 = timing2;
timing2 = MPI_Wtime();
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Prepared Matcher indexes in " << (timing2-timing1) << " seconds");
ReadSet finalContigs;
ReadSet contigs;
contigs.appendFastaFile(contigFile, world.rank(), world.size());
int maxContigsPerBatch = DistributedNucleatingAssemblerOptions::getOptions().getMaxContigsPerBatch();
short iteration = 0;
while (++iteration <= maxIterations) {
LOG_DEBUG_GATHER(1, "Iteration " << iteration << " " << MemoryUtils::getMemoryUsage());
int batchIdx = 0;
matcher->resetTimes("Start Iteration", MPI_Wtime());
setGlobalReadSetConstants(world, contigs);
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Iteration: " << iteration << ". Contig File: " << contigFile << ". contains " << contigs.getGlobalSize() << " Reads");
if (contigs.getGlobalSize() == 0) {
LOG_VERBOSE_OPTIONAL(1, true, "There are no contigs to extend in " << contigFile);
break;
}
std::string extendLog;
ReadSet changedContigs;
int lastBatch = contigs.getSize();
MPI_Allreduce(MPI_IN_PLACE, &lastBatch, 1, MPI_INT, MPI_MAX, world);
LOG_DEBUG_OPTIONAL(1, world.rank() == 0, "Iteration: " << iteration << " Last batch is " << lastBatch);
while (batchIdx < lastBatch) {
extendLog += runPartialBatch(world, matcher, contigs, contigFile, changedContigs, finalContigs, batchIdx, maxContigsPerBatch, minKmerSize, minimumCoverage, maxKmerSize, maxExtend, kmerStep);
batchIdx += maxContigsPerBatch;
}
matcher->recordTime("extendContigs", MPI_Wtime());
LOG_DEBUG_GATHER(1, (extendLog));
finishLongContigs(DistributedNucleatingAssemblerOptions::getOptions().getMaxContigLength(), changedContigs, finalContigs);
LOG_DEBUG_GATHER(1, "Changed contigs: " << changedContigs.getSize() << " finalContigs: " << finalContigs.getSize());
setGlobalReadSetConstants(world, changedContigs);
setGlobalReadSetConstants(world, finalContigs);
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Changed contigs: " << changedContigs.getGlobalSize() << " finalContigs: " << finalContigs.getGlobalSize());
std::string oldFinalContigFile = finalContigFile;
std::string oldContigFile = contigFile;
{
// write out the state of the contig files (so far) so we do not loose them
DistributedOfstreamMap om(world,
Options::getOptions().getOutputFile(), "");
om.setBuildInMemory();
if (finalContigs.getGlobalSize() > 0) {
std::string fileKey = "final-" + boost::lexical_cast<
std::string>(iteration);
finalContigs.writeAll(om.getOfstream(fileKey),
FormatOutput::Fasta());
finalContigFile = om.getRealFilePath(fileKey);
}
if (changedContigs.getGlobalSize() > 0) {
std::string filekey = "-inputcontigs-" + boost::lexical_cast<
std::string>(iteration) + ".fasta";
changedContigs.writeAll(om.getOfstream(filekey),
FormatOutput::Fasta());
contigFile = om.getRealFilePath(filekey);
}
contigs = changedContigs;
}
if (world.rank() == 0) {
// preserve the final contigs in case of crash
unlink(Options::getOptions().getOutputFile().c_str());
link(finalContigFile.c_str(), Options::getOptions().getOutputFile().c_str());
}
matcher->recordTime("writeFinalTime", MPI_Wtime());
if (!Log::isDebug(1) && world.rank() == 0) {
// remove most recent contig files (if not debugging)
if (!oldFinalContigFile.empty()) {
LOG_VERBOSE_OPTIONAL(1, true, "Removing " << oldFinalContigFile);
unlink(oldFinalContigFile.c_str());
}
if (ContigExtenderBaseOptions::getOptions().getContigFile().compare(
oldContigFile) != 0) {
LOG_VERBOSE_OPTIONAL(1, true, "Removing " << oldContigFile);
unlink(oldContigFile.c_str());
}
}
if (changedContigs.getGlobalSize() == 0) {
LOG_VERBOSE_OPTIONAL(1, world.rank() == 1, "No more contigs to extend " << changedContigs.getSize());
break;
}
matcher->recordTime("finishIteration", MPI_Wtime());
LOG_DEBUG_GATHER(1, matcher->getTimes("") + ". " + MemoryUtils::getMemoryUsage());
}
matcher.reset(); // release the matcher interface
if (world.rank() == 0 && !Log::isDebug(1)) {
if (ContigExtenderBaseOptions::getOptions().getContigFile().compare(
contigFile) != 0) {
LOG_DEBUG_OPTIONAL(1, true, "Removing " << contigFile);
unlink(contigFile.c_str());
}
}
// write final contigs (and any unfinished contigs still remaining)
finalContigs.append(contigs);
std::string tmpFinalFile = DistributedOfstreamMap::writeGlobalReadSet(world, finalContigs, Options::getOptions().getOutputFile(), ".tmp", FormatOutput::Fasta());
if (world.rank() == 0 && !finalContigFile.empty()) {
LOG_DEBUG_OPTIONAL(1, true, "Removing " << finalContigFile);
unlink(finalContigFile.c_str());
}
finalContigFile = tmpFinalFile;
if (world.rank() == 0) {
unlink(Options::getOptions().getOutputFile().c_str());
rename(finalContigFile.c_str(), Options::getOptions().getOutputFile().c_str());
}
finalContigFile = Options::getOptions().getOutputFile();
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Final contigs are in: " << finalContigFile);
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Finished");
ForkDaemon::finalize();
} catch (std::exception &e) {
LOG_ERROR(1, "DistributedNucleatingAssembler threw an exception! Aborting..." << e.what());
world.abort(1);
} catch (...) {
LOG_ERROR(1, "DistributedNucleatingAssembler threw an error!" );
world.abort(1);
}
return 0;
}
int main(int argc, char *argv[]) {
ScopedMPIComm< MPIEstimateSizeOptions > world(argc, argv);
Cleanup::prepare();
try {
MemoryUtils::getMemoryUsage();
std::string outputFilename = Options::getOptions().getOutputFile();
OptionsBaseInterface::FileListType &inputs = Options::getOptions().getInputFiles();
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Reading Input Files");
long partitions = MPIEstimateSizeOptions::getOptions().getSamplePartitions();
double maxFraction = MPIEstimateSizeOptions::getOptions().getMaxSampleFraction();
assert(maxFraction < 1.0);
double fraction = 0.0;
long totalPartitions = (long) partitions / maxFraction;
unsigned long totalReads = 0;
unsigned long totalBases = 0;
long rawKmers = 0;
KS spectrum(world, 0);
for (long iter = 0 ; iter < partitions && fraction < maxFraction; iter++) {
fraction += (double) 1. / (double) totalPartitions;
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Starting iteration " << iter << " at " << fraction*100 << "%");
ReadSet reads;
reads.appendAllFiles(inputs, world.rank()*totalPartitions + iter, world.size()*totalPartitions);
setGlobalReadSetConstants(world, reads);
unsigned long counts[3], totalCounts[3];
mpi::all_reduce(world, (unsigned long*) counts, 3, (unsigned long*) totalCounts, std::plus<unsigned long>());
totalReads += totalCounts[0];
totalBases += totalCounts[2];
if (KmerBaseOptions::getOptions().getKmerSize() > 0) {
// lazy allocate
if (rawKmers == 0) {
rawKmers = KS::estimateRawKmers(world, inputs);
spectrum = KS(world, rawKmers);
}
spectrum.buildKmerSpectrum(reads);
spectrum.trackSpectrum(true);
LOG_DEBUG_OPTIONAL(1, true, "SizeTracker: " << spectrum.getSizeTracker().toString());
if (Log::isDebug(1)) {
KS::MPIHistogram h = spectrum._getHistogram(false);
std::string hist = h.toString();
LOG_DEBUG_OPTIONAL(1, world.rank() == 0, "Collective Kmer Histogram\n" << hist);
}
}
}
std::string hist = spectrum.getHistogram(false);
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Collective Kmer Histogram\n" << hist);
KS::SizeTracker reducedSizeTracker = spectrum.reduceSizeTracker(world);
std::string reducedSizeTrackerFile = outputFilename;
if (reducedSizeTrackerFile.empty()) {
reducedSizeTrackerFile = UniqueName::generateUniqueName("tmp-estimateSize");
}
float errorRate = TrackingData::getErrorRate();
LOG_DEBUG_OPTIONAL(1, true, "Kmer error rate: " << errorRate);
float commonErrorRate = 0.0;
MPI_Reduce(&errorRate, &commonErrorRate, 1, MPI_FLOAT, MPI_SUM, 0, world);
commonErrorRate /= (float) world.size();
if (world.rank() == 0) {
{
LOG_VERBOSE_OPTIONAL(1, true, "Writing size tracking file to:" << reducedSizeTrackerFile);
LOG_DEBUG_OPTIONAL(1, true, "SizeTracker:\n" << reducedSizeTracker.toString());
OfstreamMap ofm(reducedSizeTrackerFile, "");
ofm.getOfstream("") << reducedSizeTracker.toString();
}
std::string basePath = FileUtils::getBasePath(argv[0]);
std::stringstream cmdss;
cmdss << "Rscript " << basePath << "/EstimateSize.R " << reducedSizeTrackerFile; // << " " << (commonErrorRate*1.25);
std::string command = cmdss.str();
if (!FileUtils::getBasePath("Rscript").empty() || basePath.empty()) {
LOG_DEBUG_OPTIONAL(1, true, "Executing: " << command);
IPipestream ipipe(command);
double errorRate = 0.0, genomeSize = 0.0;
bool readValues = false;
while (ipipe.good() && !ipipe.eof()) {
std::string line;
std::getline(ipipe, line);
LOG_DEBUG_OPTIONAL(2, true, "Read: " << line);
if (line.find("errorRate") != std::string::npos) {
LOG_DEBUG_OPTIONAL(2, true, "Found headers in: " << line);
readValues = true;
continue;
}
if (readValues) {
readValues = false;
LOG_DEBUG_OPTIONAL(2, true, "Reading errorRate and GenomeSize from " << line);
std::stringstream ss;
ss << line;
ss >> errorRate;
ss >> genomeSize;
}
}
LOG_VERBOSE_OPTIONAL(1, true, "Estimated Kmer-quality errorRate: " << commonErrorRate);
LOG_VERBOSE_OPTIONAL(1, true, "Distributed readCount: " << totalReads);
LOG_VERBOSE_OPTIONAL(1, true, "Estimated fractionRead: " << fraction);
LOG_VERBOSE_OPTIONAL(1, true, "Estimated errorRate: " << errorRate);
LOG_VERBOSE_OPTIONAL(1, true, "Estimated genomeSize: " << genomeSize);
ipipe.close();
double totalRawKmers = reducedSizeTracker.getLastElement().rawKmers / fraction;
double estimatedUniqueKmers = totalRawKmers * errorRate + genomeSize;
LOG_VERBOSE_OPTIONAL(1, true, "Estimated totalRawKmers: " << totalRawKmers);
LOG_VERBOSE_OPTIONAL(1, true, "Estimated totalUniqueKmers: " << estimatedUniqueKmers);
if (reducedSizeTrackerFile.compare(outputFilename) != 0) {
LOG_DEBUG_OPTIONAL(1, true, "Removing temporary size tracking file: " << reducedSizeTrackerFile);
unlink(reducedSizeTrackerFile.c_str());
}
} else {