try: qvtable = flow_space_recal.base_recalib( env['SIGPROC_RESULTS'], env['prebasecallerArgs'], env['libraryKey'], env['tfKey'], env['runID'], env['flowOrder'], env['reverse_primer_dict'], env['BASECALLER_RESULTS'], env['barcodeId'], env['barcodeSamples'], env.get('barcodesplit_filter', 0), env.get('barcodesplit_filter_minreads', 0), env['DIR_BC_FILES'], os.path.join("barcodeList.txt"), os.path.join(env['BASECALLER_RESULTS'], "barcodeMask.bin"), env['libraryName'], env['sample'], env['site_name'], env['notes'], env['start_time'], env['chipType'], env['expName'], env['resultsName'], env['pgmName'], env['tmap_version'], "datasets_basecaller.json", # file containing all available datasets "BaseCaller.json" #file containing dimension info (offsets, rows, cols) and flow info for stratification ) printtime("QVTable: %s" % qvtable)
set_result_status('Flow Space Recalibration') try: qvtable = flow_space_recal.base_recalib( env['SIGPROC_RESULTS'], env['prebasecallerArgs'], env['libraryKey'], env['tfKey'], env['runID'], env['flowOrder'], env['reverse_primer_dict'], env['BASECALLER_RESULTS'], env['barcodeId'], env['barcodeSamples'], env['barcodesplit_filter'], env['DIR_BC_FILES'], os.path.join("barcodeList.txt"), os.path.join(env['BASECALLER_RESULTS'], "barcodeMask.bin"), env['libraryName'], env['sample'], env['site_name'], env['notes'], env['start_time'], env['chipType'], env['expName'], env['resultsName'], env['pgmName'], env['tmap_version'], "datasets_basecaller.json", # file containing all available datasets "BaseCaller.json" #file containing dimension info (offsets, rows, cols) and flow info for stratification ) printtime("QVTable: %s" % qvtable) additional_basecallerArgs = " --calibration-file " + qvtable + " --phase-estimation-file " + os.path.join(env['BASECALLER_RESULTS'], "recalibration", "BaseCaller.json") + " --model-file " + os.path.join(env['BASECALLER_RESULTS'], "recalibration", "hpModel.txt")
# traceback.print_exc() if env['libraryName']=='none' or len(env['libraryName'])<1: printtime("DEBUG: No reference specified - Flow Space Recalibration skipped") else: printtime("DEBUG: Flow Space Recalibration with Reference: %s" % env['libraryName']) try: flow_space_recal.base_recalib(env['BASECALLER_RESULTS'], env['runID'], env['align_full'], env['DIR_BC_FILES'], env['libraryName'], env['sample'], env['chipType'], env['site_name'], env['flows'], env['notes'], env['barcodeId'], env['aligner_opts_extra'], env['mark_duplicates'], env['start_time'], env['tmap_version'], "datasets_basecaller.json", # file containing all available datasets "BaseCaller.json" #file containing dimension info (offsets, rows, cols) and flow info for stratification ) except: printtime("ERROR: Flow Space Recalibration Failed") else: printtime("DEBUG: Flow Space Recalibration is disabled") # create analysis progress bar file f = open('progress.txt','w')