try:
sigproc.mergeAvgNukeTraces(dirs, env['SIGPROC_RESULTS'], env['libraryKey'], 'Library Beads')
except:
printtime("Warning: mergeAvgNukeTraces '%s' 'Library Beads' failed" % env['libraryKey'])
try:
sigproc.mergeAvgNukeTraces(dirs, env['SIGPROC_RESULTS'], env['tfKey'], 'Test Fragment Beads')
except:
printtime("Warning: mergeAvgNukeTraces '%s' 'Test Fragment Beads' failed" % env['tfKey'])
try:
sigproc.generate_raw_data_traces(
env['libraryKey'],
env['tfKey'],
env['flowOrder'],
env['SIGPROC_RESULTS'])
except:
traceback.print_exc()
try:
# Only merge standard json files
basecaller.merge_datasets_basecaller_json(
dirs,
env['BASECALLER_RESULTS'])
basecaller.merge_basecaller_json(
dirs,
env['BASECALLER_RESULTS'])
except:
f.close()
os.chmod(
os.path.join(env['SIGPROC_RESULTS'],
"analysis_return_code.txt"), 0775)
except:
traceback.print_exc()
if status != 0:
printtime("ERROR: Analysis finished with status '%s'" % status)
sys.exit(1)
if args.do_basecalling:
# Generate files needed for regular and fromWells reports
sigproc.generate_raw_data_traces(env['libraryKey'], env['tfKey'],
env['flowOrder'],
env['SIGPROC_RESULTS'])
# Update or generate Bead density plots
bfmaskPath = os.path.join(env['SIGPROC_RESULTS'],
"analysis.bfmask.bin")
bfmaskstatspath = os.path.join(env['SIGPROC_RESULTS'],
"analysis.bfmask.stats")
try:
upload_analysismetrics(bfmaskstatspath)
update_bfmask_artifacts(bfmaskPath,
bfmaskstatspath,
"./",
plot_title=env['shortRunName'])
except:
traceback.print_exc()
printtime(
"Warning: mergeAvgNukeTraces '%s' 'Library Beads' failed" %
env["libraryKey"])
try:
sigproc.mergeAvgNukeTraces(dirs, env["SIGPROC_RESULTS"],
env["tfKey"], "Test Fragment Beads")
except Exception:
printtime(
"Warning: mergeAvgNukeTraces '%s' 'Test Fragment Beads' failed"
% env["tfKey"])
try:
sigproc.generate_raw_data_traces(
env["libraryKey"],
env["tfKey"],
env["flowOrder"],
env["SIGPROC_RESULTS"],
)
except Exception:
traceback.print_exc()
try:
# Only merge standard json files
basecaller.merge_datasets_basecaller_json(
dirs, env["BASECALLER_RESULTS"])
basecaller.merge_basecaller_json(dirs, env["BASECALLER_RESULTS"])
basecaller.merge_EndBarcodeReadCounts(dirs,
env["BASECALLER_RESULTS"])
except Exception:
traceback.print_exc()
printtime("ERROR: Merge Basecaller Results failed")
