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')
