void Genome::genomeLoad(){//allocate and load Genome time_t rawtime; time ( &rawtime ); *(P->inOut->logStdOut) << timeMonthDayTime(rawtime) << " ..... Loading genome\n" <<flush; uint *shmNG=NULL, *shmNSA=NULL; //pointers to shm stored values , *shmSG, *shmSSA uint64 shmSize=0;//, shmStartG=0; shmStartSA=0; uint L=200,K=6; Parameters *P1 = new Parameters; ifstream parFile((P->genomeDir+("/genomeParameters.txt")).c_str()); if (parFile.good()) { P->inOut->logMain << "Reading genome generation parameters:\n"; P1->inOut = P->inOut; P1->scanAllLines(parFile,3,-1); parFile.close(); } else { ostringstream errOut; errOut << "EXITING because of FATAL ERROR: could not open genome file "<< P->genomeDir+("/genomeParameters.txt") << endl; errOut << "SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions\n" <<flush; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P); }; //check genome version if (P1->versionGenome.size()==0 || P1->versionGenome[0]==0) {// ostringstream errOut; errOut << "EXITING because of FATAL ERROR: read no value for the versionGenome parameter from genomeParameters.txt file\n"; errOut << "SOLUTION: please re-generate genome from scratch with the latest version of STAR\n"; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P); } else if (P->sjdbFileChrStartEnd.at(0)=="-" && P1->versionGenome.at(0) >= P->versionGenome.at(0)) {// P->inOut->logMain << "Genome version is compatible with current STAR version\n"; } else if (P->sjdbFileChrStartEnd.at(0)!="-" && P1->versionGenome.at(0) >= P->versionGenome.at(1)) {// P->inOut->logMain << "Genome version is compatible with current STAR version\n"; } else { ostringstream errOut; errOut << "EXITING because of FATAL ERROR: Genome version is INCOMPATIBLE with current STAR version\n"; errOut << "SOLUTION: please re-generate genome from scratch with the latest version of STAR\n"; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P); }; //check if sjdbInfo.txt exists => genome was generated with junctions bool sjdbInfoExists=false; struct stat sjdb1; if ( stat( (P->genomeDir+"/sjdbInfo.txt").c_str(), &sjdb1) == 0 ) {//file exists sjdbInfoExists=true; }; if ( P->sjdbInsert.yes && sjdbInfoExists && P1->sjdbInsert.save=="") {//if sjdbInsert, and genome had junctions, and genome is old - it should be re-generated with new STAR ostringstream errOut; errOut << "EXITING because of FATAL ERROR: old Genome is INCOMPATIBLE with on the fly junction insertion\n"; errOut << "SOLUTION: please re-generate genome from scratch with the latest version of STAR\n"; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P); }; //record required genome parameters in P P->genomeSAindexNbases=P1->genomeSAindexNbases; P->genomeChrBinNbits=P1->genomeChrBinNbits; P->genomeSAsparseD=P1->genomeSAsparseD; if (P->parArray.at(P->sjdbOverhang_par)->inputLevel==0 && P1->sjdbOverhang>0) {//if --sjdbOverhang was not defined by user and it was defined >0 at the genome generation step, then use sjdbOverhang from the genome generation step P->sjdbOverhang=P1->sjdbOverhang; P->inOut->logMain << "--sjdbOverhang = " << P->sjdbOverhang << " taken from the generated genome\n"; } else if (sjdbInfoExists && P->parArray.at(P->sjdbOverhang_par)->inputLevel>0 && P->sjdbOverhang!=P1->sjdbOverhang) {//if sjdbOverhang was defined at the genome generation step,the mapping step value has to agree with it ostringstream errOut; errOut << "EXITING because of fatal PARAMETERS error: present --sjdbOverhang="<<P->sjdbOverhang << " is not equal to the value at the genome generation step ="<< P1->sjdbOverhang << "\n"; errOut << "SOLUTION: \n" <<flush; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P); }; P->sjdbLength = P->sjdbOverhang==0 ? 0 : P->sjdbOverhang*2+1; P->inOut->logMain << "Started loading the genome: " << asctime (localtime ( &rawtime ))<<"\n"<<flush; ifstream GenomeIn, SAin, SAiIn; P->nGenome = OpenStream("Genome",GenomeIn); P->nSAbyte = OpenStream("SA",SAin); OpenStream("/SAindex",SAiIn); uint SAiInBytes=0; SAiInBytes += fstreamReadBig(SAiIn,(char*) &P->genomeSAindexNbases, sizeof(P->genomeSAindexNbases)); P->genomeSAindexStart = new uint[P->genomeSAindexNbases+1]; SAiInBytes += fstreamReadBig(SAiIn,(char*) P->genomeSAindexStart, sizeof(P->genomeSAindexStart[0])*(P->genomeSAindexNbases+1)); P->nSAi=P->genomeSAindexStart[P->genomeSAindexNbases]; P->inOut->logMain << "Read from SAindex: genomeSAindexNbases=" << P->genomeSAindexNbases <<" nSAi="<< P->nSAi <<endl; /////////////////////////////////// at this point all array sizes should be known: calculate packed array lengths P->GstrandBit = (uint) floor(log(P->nGenome)/log(2))+1; if (P->GstrandBit<32) P->GstrandBit=32; //TODO: use simple access function for SA P->GstrandMask = ~(1LLU<<P->GstrandBit); P->nSA=(P->nSAbyte*8)/(P->GstrandBit+1); SA.defineBits(P->GstrandBit+1,P->nSA); P->SAiMarkNbit=P->GstrandBit+1; P->SAiMarkAbsentBit=P->GstrandBit+2; P->SAiMarkNmaskC=1LLU << P->SAiMarkNbit; P->SAiMarkNmask=~P->SAiMarkNmaskC; P->SAiMarkAbsentMaskC=1LLU << P->SAiMarkAbsentBit; P->SAiMarkAbsentMask=~P->SAiMarkAbsentMaskC; SAi.defineBits(P->GstrandBit+3,P->nSAi); P->inOut->logMain << "nGenome=" << P->nGenome << "; nSAbyte=" << P->nSAbyte <<endl<< flush; P->inOut->logMain <<"GstrandBit="<<int(P->GstrandBit)<<" SA number of indices="<<P->nSA<<endl<<flush; shmSize=SA.lengthByte + P->nGenome+L+L+SHM_startG+8; shmSize+= SAi.lengthByte; if (P->annotScoreScale>0) shmSize+=P->nGenome; if ((P->genomeLoad=="LoadAndKeep" || P->genomeLoad=="LoadAndRemove" || P->genomeLoad=="LoadAndExit" || P->genomeLoad=="Remove") && sharedMemory == NULL) { bool unloadLast = P->genomeLoad=="LoadAndRemove"; try { sharedMemory = new SharedMemory(shmKey, unloadLast); sharedMemory->SetErrorStream(P->inOut->logStdOut); if (!sharedMemory->NeedsAllocation()) P->inOut->logMain <<"Found genome in shared memory\n"<<flush; if (P->genomeLoad=="Remove") {//kill the genome and exit if (sharedMemory->NeedsAllocation()) {//did not find genome in shared memory, nothing to kill ostringstream errOut; errOut << "EXITING: Did not find the genome in memory, did not remove any genomes from shared memory\n"; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P); } else { sharedMemory->Clean(); P->inOut->logMain <<"DONE: removed the genome from shared memory\n"<<flush; return; }; } if (sharedMemory->NeedsAllocation()){ P->inOut->logMain <<"Allocating shared memory for genome\n"<<flush; sharedMemory->Allocate(shmSize); } } catch (const SharedMemoryException & exc) { HandleSharedMemoryException(exc, shmSize); } shmStart = (char*) sharedMemory->GetMapped(); shmNG= (uint*) (shmStart+SHM_sizeG); shmNSA= (uint*) (shmStart+SHM_sizeSA); if (!sharedMemory->IsAllocator()) { // genome is in shared memory or being loaded // wait for the process that will populate it // and record the sizes uint iwait=0; while (*shmNG != P->nGenome) { iwait++; P->inOut->logMain <<"Another job is still loading the genome, sleeping for 1 min\n" <<flush; sleep(60); if (iwait==100) { ostringstream errOut; errOut << "EXITING because of FATAL ERROR: waited too long for the other job to finish loading the genome" << strerror(errno) << "\n" <<flush; errOut << "SOLUTION: remove the shared memory chunk by running STAR with --genomeLoad Remove, and restart STAR" <<flush; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_LOADING_WAITED_TOO_LONG, *P); }; }; if (P->nSAbyte!=*shmNSA) { ostringstream errOut; errOut << "EXITING because of FATAL ERROR: the SA file size did not match what we found in shared memory" << "\n" << flush; errOut << "SOLUTION: remove the shared memory chunk by running STAR with --genomeLoad Remove, and restart STAR" << flush; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INCONSISTENT_DATA, *P); } P->inOut->logMain << "Using shared memory for genome. key=0x" <<hex<<shmKey<<dec<< "; shmid="<< sharedMemory->GetId() <<endl<<flush; } G1=shmStart+SHM_startG; SA.pointArray(G1+P->nGenome+L+L); char* shmNext=SA.charArray+P->nSAbyte; SAi.pointArray(shmNext); shmNext += SAi.lengthByte; // if (twoPass.pass1readsN==0) {//not 2-pass // shmStartG=SHM_startSHM; // shmStartSA=0; // } else {//2-pass // ostringstream errOut; // errOut << "EXITING because of FATAL ERROR: 2-pass procedure cannot be used with genome already loaded im memory' "\n" ; // errOut << "SOLUTION: check shared memory settigns as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory\n" <<flush; // exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_SHM, *P); // }; if (P->annotScoreScale>0) {//optional allocation sigG = shmNext; shmNext += P->nGenome; } } else if (P->genomeLoad=="NoSharedMemory") // simply allocate memory, do not use shared memory { try { if (P->sjdbInsert.pass1 || P->sjdbInsert.pass2) {//reserve extra memory for insertion at the 1st and/or 2nd step nGenomePass1=P->nGenome; nSApass1=P->nSA; if (P->sjdbInsert.pass1) { nGenomePass1+=P->limitSjdbInsertNsj*P->sjdbLength; nSApass1+=2*P->limitSjdbInsertNsj*P->sjdbLength; }; nGenomePass2=nGenomePass1; nSApass2=nSApass1; if (P->sjdbInsert.pass2) { nGenomePass2+=P->limitSjdbInsertNsj*P->sjdbLength; nSApass2+=2*P->limitSjdbInsertNsj*P->sjdbLength; }; G1=new char[nGenomePass2+L+L]; SApass2.defineBits(P->GstrandBit+1,nSApass2); SApass2.allocateArray(); SApass1.defineBits(P->GstrandBit+1,nSApass1); SApass1.pointArray(SApass2.charArray+SApass2.lengthByte-SApass1.lengthByte); SA.pointArray(SApass1.charArray+SApass1.lengthByte-SA.lengthByte); } else {//no insertions G1=new char[P->nGenome+L+L]; SA.allocateArray(); }; SAi.allocateArray(); P->inOut->logMain <<"Shared memory is not used for genomes. Allocated a private copy of the genome.\n"<<flush; } catch (exception & exc) { ostringstream errOut; errOut <<"EXITING: fatal error trying to allocate genome arrays, exception thrown: "<<exc.what()<<endl; errOut <<"Possible cause 1: not enough RAM. Check if you have enough RAM " << P->nGenome+L+L+SA.lengthByte+SAi.lengthByte+2000000000 << " bytes\n"; errOut <<"Possible cause 2: not enough virtual memory allowed with ulimit. SOLUTION: run ulimit -v " << P->nGenome+L+L+SA.lengthByte+SAi.lengthByte+2000000000<<endl <<flush; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_MEMORY_ALLOCATION, *P); }; } // if (twopass1readsN==0) {//not 2-pass // shmStartG=SHM_startSHM; // shmStartSA=0; // } else {//2-pass // ostringstream errOut; // errOut << "EXITING because of FATAL ERROR: 2-pass procedure cannot be used with genome already loaded im memory' "\n" ; // errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory\n" <<flush; // exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_SHM, *P); // }; G=G1+L; bool isAllocatorProcess = sharedMemory != NULL && sharedMemory->IsAllocator(); if (P->genomeLoad=="NoSharedMemory" || isAllocatorProcess) {//load genome and SAs from files //load genome P->inOut->logMain <<"Genome file size: "<<P->nGenome <<" bytes; state: good=" <<GenomeIn.good()\ <<" eof="<<GenomeIn.eof()<<" fail="<<GenomeIn.fail()<<" bad="<<GenomeIn.bad()<<"\n"<<flush; P->inOut->logMain <<"Loading Genome ... " << flush; uint genomeReadBytesN=fstreamReadBig(GenomeIn,G,P->nGenome); P->inOut->logMain <<"done! state: good=" <<GenomeIn.good()\ <<" eof="<<GenomeIn.eof()<<" fail="<<GenomeIn.fail()<<" bad="<<GenomeIn.bad()<<"; loaded "<<genomeReadBytesN<<" bytes\n" << flush; GenomeIn.close(); for (uint ii=0;ii<L;ii++) {// attach a tail with the largest symbol G1[ii]=K-1; G[P->nGenome+ii]=K-1; }; //load SAs P->inOut->logMain <<"SA file size: "<<SA.lengthByte <<" bytes; state: good=" <<SAin.good()\ <<" eof="<<SAin.eof()<<" fail="<<SAin.fail()<<" bad="<<SAin.bad()<<"\n"<<flush; P->inOut->logMain <<"Loading SA ... " << flush; genomeReadBytesN=fstreamReadBig(SAin,SA.charArray, SA.lengthByte); P->inOut->logMain <<"done! state: good=" <<SAin.good()\ <<" eof="<<SAin.eof()<<" fail="<<SAin.fail()<<" bad="<<SAin.bad()<<"; loaded "<<genomeReadBytesN<<" bytes\n" << flush; SAin.close(); P->inOut->logMain <<"Loading SAindex ... " << flush; SAiInBytes +=fstreamReadBig(SAiIn,SAi.charArray, SAi.lengthByte); P->inOut->logMain <<"done: "<<SAiInBytes<<" bytes\n" << flush; }; SAiIn.close(); if ((P->genomeLoad=="LoadAndKeep" || P->genomeLoad=="LoadAndRemove" || P->genomeLoad=="LoadAndExit") && isAllocatorProcess ) { //record sizes. This marks the end of genome loading *shmNG=P->nGenome; *shmNSA=P->nSAbyte; }; time ( &rawtime ); P->inOut->logMain << "Finished loading the genome: " << asctime (localtime ( &rawtime )) <<"\n"<<flush; #ifdef COMPILE_FOR_MAC { uint sum1=0; for (uint ii=0;ii<P->nGenome; ii++) sum1 += (uint) (unsigned char) G[ii]; P->inOut->logMain << "Sum of all Genome bytes: " <<sum1 <<"\n"<<flush; sum1=0; for (uint ii=0;ii<SA.lengthByte; ii++) sum1 += (uint) (unsigned char) SA.charArray[ii]; P->inOut->logMain << "Sum of all SA bytes: " <<sum1 <<"\n"<<flush; sum1=0; for (uint ii=0;ii<SAi.lengthByte; ii++) sum1 += (uint) (unsigned char) SAi.charArray[ii]; P->inOut->logMain << "Sum of all SAi bytes: " <<sum1 <<"\n"<<flush; }; #endif if (P->genomeLoad=="LoadAndExit") { uint shmSum=0; for (uint ii=0;ii<shmSize;ii++) shmSum+=shmStart[ii]; P->inOut->logMain << "genomeLoad=LoadAndExit: completed, the genome is loaded and kept in RAM, EXITING now.\n"<<flush; // system("echo `date` ..... Finished genome loading >> Log.timing.out"); return; }; //find chr starts from files P->chrInfoLoad(); P->chrBinFill(); //splice junctions database if (P->nGenome==P->chrStart[P->nChrReal]) {//no sjdb P->sjdbN=0; P->sjGstart=P->chrStart[P->nChrReal]+1; //not sure why I need that } else {//there are sjdb chromosomes ifstream sjdbInfo((P->genomeDir+"/sjdbInfo.txt").c_str()); if (sjdbInfo.fail()) { ostringstream errOut; errOut << "EXITING because of FATAL error, could not open file " << (P->genomeDir+"/sjdbInfo.txt") <<"\n"; errOut << "SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions\n" <<flush; exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P); }; sjdbInfo >> P->sjdbN >> P->sjdbOverhang; P->inOut->logMain << "Processing splice junctions database sjdbN=" <<P->sjdbN<<", sjdbOverhang=" <<P->sjdbOverhang <<" \n"; P->sjChrStart=P->nChrReal; P->sjGstart=P->chrStart[P->sjChrStart]; //fill the sj-db to genome translation array P->sjDstart=new uint [P->sjdbN]; P->sjAstart=new uint [P->sjdbN]; P->sjdbStart=new uint [P->sjdbN]; P->sjdbEnd=new uint [P->sjdbN]; P->sjdbMotif=new uint8 [P->sjdbN]; P->sjdbShiftLeft=new uint8 [P->sjdbN]; P->sjdbShiftRight=new uint8 [P->sjdbN]; P->sjdbStrand=new uint8 [P->sjdbN]; for (uint ii=0;ii<P->sjdbN;ii++) {//get the info about junctions from sjdbInfo.txt { uint16 d1,d2,d3,d4; sjdbInfo >> P->sjdbStart[ii] >> P->sjdbEnd[ii] >> d1 >> d2 >> d3 >> d4; P->sjdbMotif[ii] = (uint8) d1; P->sjdbShiftLeft[ii] = (uint8) d2; P->sjdbShiftRight[ii] = (uint8) d3; P->sjdbStrand[ii] = (uint8) d4; }; P->sjDstart[ii] = P->sjdbStart[ii] - P->sjdbOverhang; P->sjAstart[ii] = P->sjdbEnd[ii] + 1; if (P->sjdbMotif[ii]==0) {//shinon-canonical junctions back to their true coordinates P->sjDstart[ii] += P->sjdbShiftLeft[ii]; P->sjAstart[ii] += P->sjdbShiftLeft[ii]; }; }; }; //check and redefine some parameters //max intron size if (P->alignIntronMax==0 && P->alignMatesGapMax==0) { P->inOut->logMain << "alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=" \ << (1LLU<<P->winBinNbits)*P->winAnchorDistNbins <<endl; } else { //redefine winBinNbits P->winBinNbits=max( (uint) floor(log2(P->nGenome/40000)+0.5), (uint) floor(log2(max(max(4LLU,P->alignIntronMax),P->alignMatesGapMax)/4)+0.5) ); P->inOut->logMain << "To accomodate alignIntronMax="<<P->alignIntronMax<<" redefined winBinNbits="<< P->winBinNbits <<endl; }; if (P->winBinNbits > P->genomeChrBinNbits) { P->inOut->logMain << "winBinNbits=" <<P->winBinNbits <<" > " << "genomeChrBinNbits=" << P->genomeChrBinNbits << " redefining:\n"; P->winBinNbits=P->genomeChrBinNbits; P->inOut->logMain << "winBinNbits=" <<P->winBinNbits <<endl; }; if (P->alignIntronMax==0 && P->alignMatesGapMax==0) { } else { //redefine winFlankNbins,winAnchorDistNbins P->winFlankNbins=max(P->alignIntronMax,P->alignMatesGapMax)/(1LLU<<P->winBinNbits)+1; P->winAnchorDistNbins=2*P->winFlankNbins; P->inOut->logMain << "To accomodate alignIntronMax="<<P->alignIntronMax<<" and alignMatesGapMax="<<P->alignMatesGapMax<<\ ", redefined winFlankNbins="<<P->winFlankNbins<<" and winAnchorDistNbins="<<P->winAnchorDistNbins<<endl; }; P->winBinChrNbits=P->genomeChrBinNbits-P->winBinNbits; P->winBinN = P->nGenome/(1LLU << P->winBinNbits)+1;//this may be chenaged later };
/** Loads the instrument into a workspace. */ void VesuvioL1ThetaResolution::loadInstrument() { // Get the filename for the VESUVIO IDF MatrixWorkspace_sptr tempWS = WorkspaceFactory::Instance().create("Workspace2D", 1, 1, 1); const std::string vesuvioIPF = tempWS->getInstrumentFilename("VESUVIO"); // Load an empty VESUVIO instrument workspace IAlgorithm_sptr loadInst = AlgorithmManager::Instance().create("LoadEmptyInstrument"); loadInst->initialize(); loadInst->setChild(true); loadInst->setLogging(false); loadInst->setProperty("OutputWorkspace", "__evs"); loadInst->setProperty("Filename", vesuvioIPF); loadInst->execute(); m_instWorkspace = loadInst->getProperty("OutputWorkspace"); // Load the PAR file if provided const std::string parFilename = getPropertyValue("PARFile"); if (!parFilename.empty()) { g_log.information() << "Loading PAR file: " << parFilename << '\n'; // Get header format std::map<size_t, std::string> headerFormats; headerFormats[5] = "spectrum,theta,t0,-,R"; headerFormats[6] = "spectrum,-,theta,t0,-,R"; std::ifstream parFile(parFilename); if (!parFile) { throw std::runtime_error("Cannot open PAR file"); } std::string header; getline(parFile, header); g_log.debug() << "PAR file header: " << header << '\n'; boost::trim(header); std::vector<std::string> headers; boost::split(headers, header, boost::is_any_of("\t "), boost::token_compress_on); size_t numCols = headers.size(); g_log.debug() << "PAR file columns: " << numCols << '\n'; std::string headerFormat = headerFormats[numCols]; if (headerFormat.empty()) { std::stringstream error; error << "Unrecognised PAR file header. Number of colums: " << numCols << " (expected either 5 or 6."; throw std::runtime_error(error.str()); } g_log.debug() << "PAR file header format: " << headerFormat << '\n'; // Update instrument IAlgorithm_sptr updateInst = AlgorithmManager::Instance().create("UpdateInstrumentFromFile"); updateInst->initialize(); updateInst->setChild(true); updateInst->setLogging(false); updateInst->setProperty("Workspace", m_instWorkspace); updateInst->setProperty("Filename", parFilename); updateInst->setProperty("MoveMonitors", false); updateInst->setProperty("IgnorePhi", true); updateInst->setProperty("AsciiHeader", headerFormat); updateInst->execute(); m_instWorkspace = updateInst->getProperty("Workspace"); } const int specIdxMin = static_cast<int>( m_instWorkspace->getIndexFromSpectrumNumber(getProperty("SpectrumMin"))); const int specIdxMax = static_cast<int>( m_instWorkspace->getIndexFromSpectrumNumber(getProperty("SpectrumMax"))); // Crop the workspace to just the detectors we are interested in IAlgorithm_sptr crop = AlgorithmManager::Instance().create("CropWorkspace"); crop->initialize(); crop->setChild(true); crop->setLogging(false); crop->setProperty("InputWorkspace", m_instWorkspace); crop->setProperty("OutputWorkspace", "__evs"); crop->setProperty("StartWorkspaceIndex", specIdxMin); crop->setProperty("EndWorkspaceIndex", specIdxMax); crop->execute(); m_instWorkspace = crop->getProperty("OutputWorkspace"); m_sample = m_instWorkspace->getInstrument()->getSample(); }