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")