def create_bcl2fastq_command_line(run_id, command_path, input_run_data_path, fastq_output_dir, samplesheet_csv_path,
tmp_path, nb_mismatch, conf):
nb_threads = str(get_cpu_count(conf))
if command_path is None:
final_command_path = 'bcl2fastq'
else:
final_command_path = command_path
# List arg
args = []
args.append(final_command_path)
args.extend(['--loading-threads', nb_threads])
args.extend(['--demultiplexing-threads', nb_threads])
args.extend(['--processing-threads', nb_threads])
args.extend(['--writing-threads', nb_threads])
args.extend(['--sample-sheet', samplesheet_csv_path])
args.extend(['--barcode-mismatches', nb_mismatch])
# Common parameter, setting per default
args.extend(['--input-dir', quote(input_run_data_path + '/Data/Intensities/BaseCalls')])
args.extend(['--output-dir', quote(fastq_output_dir)])
if common.is_conf_value_equals_true(BCL2FASTQ_WITH_FAILED_READS_KEY, conf):
args.append('--with-failed-reads')
# Specific parameter
args.extend(['--runfolder-dir', quote(input_run_data_path)])
args.extend(['--interop-dir', quote(fastq_output_dir + '/InterOp')])
args.extend(['--min-log-level', 'TRACE'])
# args.extend(['--stats-dir', fastq_output_dir + '/Stats'])
# args.extend(['--reports-dir', fastq_output_dir + '/Reports'])
# Set the compression level
if common.is_conf_key_exists(BCL2FASTQ_COMPRESSION_LEVEL_KEY, conf):
level_str = conf[BCL2FASTQ_COMPRESSION_LEVEL_KEY].strip()
try:
level_int = int(level_str)
if level_int > 0 and level_int < 10:
args.extend(['--fastq-compression-level', str(level_int)])
except ValueError:
pass
if common.is_conf_key_exists(BCL2FASTQ_ADDITIONNAL_ARGUMENTS_KEY, conf):
additional_args = conf[BCL2FASTQ_ADDITIONNAL_ARGUMENTS_KEY]
additional_args = re.sub('\\s+', ' ', additional_args).strip()
args.extends(additional_args.split(' '))
# Retrieve output in file
args.extend(['>', quote(tmp_path + '/bcl2fastq_output_' + run_id + '.out')])
args.extend(['2>', quote(tmp_path + '/bcl2fastq_output_' + run_id + '.err')])
return " ".join(args)
def is_sync_step_enable(conf):
"""Check if all parameters useful for synchronization step are defined
Arguments:
conf: configuration dictionary
"""
# Synchronization step: True
if common.is_conf_value_equals_true(SYNC_STEP_KEY, conf):
# Check bcl path must be defined
if common.is_conf_key_exists(BCL_DATA_PATH_KEY, conf):
bcl_path = conf[BCL_DATA_PATH_KEY]
# Check bcl not same hiseq output path
for path in hiseq_run.get_hiseq_data_paths(conf):
if path == bcl_path:
error('Configuration error.',
'Basecalling path and hiseq output data path must be different: ' + bcl_path, conf)
return False
return True
return False
def demux(run_id, conf):
"""Add a processed run id to the list of the run ids.
Arguments:
run_id: The run id
conf: configuration dictionary
"""
start_time = time.time()
common.log('INFO', 'Demux step: Starting', conf)
reports_data_base_path = conf[REPORTS_DATA_PATH_KEY]
reports_data_path = common.get_report_run_data_path(run_id, conf)
samplesheet_filename = build_samplesheet_filename(run_id, conf)
bcl2fastq_samplesheet_path = conf[TMP_PATH_KEY] + '/' + samplesheet_filename + '.csv'
input_run_data_path = common.get_input_run_data_path(run_id, conf)
if input_run_data_path is None:
return False
fastq_output_dir = conf[FASTQ_DATA_PATH_KEY] + '/' + run_id
basecall_stats_prefix = 'basecall_stats_'
basecall_stats_file = basecall_stats_prefix + run_id + '.tar.bz2'
# Check if root input bcl data directory exists
if not os.path.exists(input_run_data_path):
error("Basecalling data directory does not exist",
"Basecalling data directory does not exist: " + str(input_run_data_path), conf)
# return False
# Check if root input fastq data directory exists
if not common.is_dir_exists(FASTQ_DATA_PATH_KEY, conf):
error("FASTQ data directory does not exist",
"FASTQ data directory does not exist: " + conf[FASTQ_DATA_PATH_KEY], conf)
return False
# Check if bcl2fastq samplesheets path exists
if not common.is_dir_exists(BCL2FASTQ_SAMPLESHEETS_PATH_KEY, conf):
error("Bcl2fastq samplesheet directory does not exist",
"Bcl2fastq samplesheet directory does not exist: " + conf[BCL2FASTQ_SAMPLESHEETS_PATH_KEY], conf)
return False
# Check if bcl2fastq basedir path exists
if not common.is_conf_value_equals_true(BCL2FASTQ_USE_DOCKER_KEY, conf):
if not common.is_dir_exists(BCL2FASTQ_PATH_KEY, conf):
error("Bcl2fastq directory does not exist",
"Bcl2fastq directory does not exist: " + conf[BCL2FASTQ_PATH_KEY], conf)
return False
# Check if temporary directory exists
if not common.is_dir_exists(TMP_PATH_KEY, conf):
error("Temporary directory does not exist",
"Temporary directory does not exist: " + conf[TMP_PATH_KEY], conf)
return False
# Check if reports_data_path exists
if not os.path.exists(reports_data_base_path):
error("Report directory does not exist",
"Report directory does not exist: " + reports_data_base_path, conf)
return False
# Create if not exist report directory for the run
if not os.path.exists(reports_data_path):
os.mkdir(reports_data_path)
# Check if basecall stats archive exists
if os.path.exists(reports_data_path + '/' + basecall_stats_file):
error('Basecall stats archive already exists for run ' + run_id,
'Basecall stats archive already exists for run ' + run_id + ': ' + basecall_stats_file, conf)
return False
# Check if the output directory already exists
if os.path.exists(fastq_output_dir):
error("FASTQ output directory already exists for run " + run_id,
'FASTQ output directory already exists for run ' + run_id + ': ' + fastq_output_dir, conf)
return False
# Compute disk usage and disk free to check if enough disk space is available
input_path_du = common.du(input_run_data_path)
output_df = common.df(conf[FASTQ_DATA_PATH_KEY])
du_factor = float(conf[DEMUX_SPACE_FACTOR_KEY])
space_needed = input_path_du * du_factor
common.log("WARNING", "Demux step: input disk usage: " + str(input_path_du), conf)
common.log("WARNING", "Demux step: output disk free: " + str(output_df), conf)
common.log("WARNING", "Demux step: space needed: " + str(space_needed), conf)
common.log("CONFIG", "Bcl2fastq Docker mode: " + str(
common.is_conf_value_equals_true(Settings.BCL2FASTQ_USE_DOCKER_KEY, conf)), conf)
# Check if free space is available
if output_df < space_needed:
error("Not enough disk space to perform demultiplexing for run " + run_id,
"Not enough disk space to perform demultiplexing for run " + run_id +
'.\n%.2f Gb' % (space_needed / 1024 / 1024 / 1024) + ' is needed (factor x' + str(
du_factor) + ') on ' + fastq_output_dir + '.', conf)
return False
# Load RunInfo object
run_info = RunInfo.parse(input_run_data_path + '/RunInfo.xml')
# Load samplesheet
samplesheet, original_samplesheet_path = load_samplesheet(run_id, input_run_data_path, samplesheet_filename, conf)
if samplesheet is None:
return False
# Update samplesheet
if not update_samplesheet(samplesheet, run_id, run_info.getFlowCellLaneCount(), conf):
return False
# Check samplesheet
check_result, samplesheet_warnings = check_samplesheet(samplesheet, run_id, run_info.getFlowCell(), conf)
if not check_result:
return False
# Get the number of mismatches
nb_mismatch = get_bcl2fastq_mismatches(samplesheet, conf[BCL2FASTQ_MISMATCHES_KEY])
# Write final samplesheet
if not write_bcl2fastq_samplesheet(samplesheet, bcl2fastq_samplesheet_path, conf):
return False
# Run demultiplexing
if common.is_conf_value_equals_true(Settings.BCL2FASTQ_USE_DOCKER_KEY, conf):
# With image docker
if not demux_run_with_docker(run_id, input_run_data_path, fastq_output_dir, bcl2fastq_samplesheet_path,
nb_mismatch, conf):
return False
else:
if not demux_run_standalone(run_id, input_run_data_path, fastq_output_dir, bcl2fastq_samplesheet_path,
nb_mismatch, conf):
return False
# Check if the output directory has been created
if not os.path.exists(fastq_output_dir):
error("Error while demultiplexing run " + run_id + ' on ' + common.get_instrument_name(run_id, conf),
'Error while demultiplexing run ' + run_id + '.\n' +
'The output directory of bcl2fastq has been created: ' + fastq_output_dir, conf)
return False
# Check if the output directory has been created
if os.path.isfile(fastq_output_dir):
error("Error while demultiplexing run " + run_id + ' on ' + common.get_instrument_name(run_id, conf),
'Error while demultiplexing run ' + run_id + '.\n' +
'The output directory of bcl2fastq is a file instead of a directory: ' + fastq_output_dir, conf)
return False
# Copy bcl2fastq log to output directory
cmd = 'cp ' + quote(conf[TMP_PATH_KEY]) + '/bcl2fastq_output_' + run_id + '.* ' + quote(fastq_output_dir)
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error("Error while copying bcl2fastq log to the output FASTQ directory" + run_id_msg,
'Error while copying bcl2fastq log to the output FASTQ directory.\nCommand line:\n' + cmd, conf)
return False
# The output directory must be read only
if not common.chmod_files_in_dir(fastq_output_dir, ".fastq", conf):
error("Error while setting the output FASTQ directory to read only" + run_id_msg,
'Error while setting the output FASTQ directory to read only.\nCommand line:\n' + cmd, conf)
return False
if not check_if_output_fastq_files_exists(fastq_output_dir):
error("Error with bcl2fastq execution for run " + run_id,
"Error with bcl2fastq execution for run " + run_id + " no FASTQ file found in " + fastq_output_dir,
conf)
return False
# Copy samplesheet to output directory
cmd = 'cp -p ' + quote(bcl2fastq_samplesheet_path) + ' ' + quote(fastq_output_dir + '/SampleSheet.csv')
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error("Error while copying samplesheet file to FASTQ directory for run " + run_id,
'Error while copying samplesheet file to FASTQ directory.\nCommand line:\n' + cmd, conf)
return False
# Create archives on demultiplexing statistics
if not archive_demux_stat(run_id, fastq_output_dir, reports_data_path, basecall_stats_file,
basecall_stats_prefix, bcl2fastq_samplesheet_path, conf):
return False
# Archive samplesheet
if not archive_samplesheet(run_id, original_samplesheet_path, bcl2fastq_samplesheet_path, conf):
return False
# Remove temporary samplesheet files
if os.path.exists(bcl2fastq_samplesheet_path):
os.remove(bcl2fastq_samplesheet_path)
# Create index.hml file
common.create_html_index_file(conf, run_id, [Settings.HISEQ_STEP_KEY, Settings.DEMUX_STEP_KEY])
df_in_bytes = common.df(fastq_output_dir)
du_in_bytes = common.du(fastq_output_dir)
df = df_in_bytes / (1024 * 1024 * 1024)
du = du_in_bytes / (1024 * 1024 * 1024)
common.log("WARNING", "Demux step: output disk free after demux: " + str(df_in_bytes), conf)
common.log("WARNING", "Demux step: space used by demux: " + str(du_in_bytes), conf)
duration = time.time() - start_time
msg = 'Ending demultiplexing with ' + nb_mismatch + ' mismatch(es) for run ' + run_id + '.' + \
'\nJob finished at ' + common.time_to_human_readable(time.time()) + \
' without error in ' + common.duration_to_human_readable(duration) + '.\n\n' + \
'FASTQ files for this run ' + \
'can be found in the following directory:\n ' + fastq_output_dir
if samplesheet_warnings.size() > 0:
msg += '\n\nSamplesheet warnings:'
for warn in samplesheet_warnings:
msg += "\n - " + warn
# Add path to report if reports.url exists
if common.is_conf_key_exists(REPORTS_URL_KEY, conf):
msg += '\n\nRun reports can be found at following location:\n ' + conf[REPORTS_URL_KEY] + '/' + run_id
msg += '\n\nFor this task %.2f GB has been used and %.2f GB still free.' % (du, df)
common.send_msg('[Aozan] Ending demultiplexing for run ' + run_id + ' on ' +
common.get_instrument_name(run_id, conf), msg, False, conf)
common.log('INFO', 'Demux step: successful in ' + common.duration_to_human_readable(duration), conf)
return True
def load_samplesheet(run_id, input_run_data_path, samplesheet_filename, conf):
""" Load the samplesheet.
Arguments:
run id: The run id
input_run_data_path: The input run data path
samplesheet_filename: samplesheet filename
conf: configuration dictionary
Return:
a Samplesheet object and the original path of the samplesheet
"""
run_info_path = input_run_data_path + '/RunInfo.xml'
if not os.path.isfile(run_info_path):
error("no RunInfo.xml file found for run " + run_id,
"No RunInfo.xml file found for run " + run_id + ': ' + run_info_path + '.\n', conf)
return None, None
run_info = RunInfo.parse(run_info_path)
flow_cell_id = run_info.getFlowCell()
common.log("INFO", "Flowcell id: " + flow_cell_id, conf)
common.log("INFO", "Samplesheet format: " + str(conf[BCL2FASTQ_SAMPLESHEET_FORMAT_KEY]), conf)
try:
if common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xls', conf):
return load_samplesheet_using_extension(conf,samplesheet_filename,'xls',input_run_data_path,run_id)
elif common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'csv', conf):
return load_samplesheet_using_extension(conf,samplesheet_filename,'csv',input_run_data_path,run_id)
elif common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'xlsx', conf):
return load_samplesheet_using_extension(conf,samplesheet_filename,'xlsx',input_run_data_path,run_id)
elif common.is_conf_value_defined(BCL2FASTQ_SAMPLESHEET_FORMAT_KEY, 'command', conf):
action_error_msg = 'Error while creating Bcl2fastq CSV samplesheet file'
if not common.is_conf_key_exists(BCL2FASTQ_SAMPLESHEET_GENERATOR_COMMAND_KEY, conf):
error(action_error_msg + ' for run ' + run_id, action_error_msg + ' the command is empty.', conf)
return None, None
input_samplesheet_generated_path = conf[TMP_PATH_KEY] + '/' + samplesheet_filename + 'generated.csv'
cmd = conf[
BCL2FASTQ_SAMPLESHEET_GENERATOR_COMMAND_KEY] + ' ' + run_id + ' ' + quote(input_samplesheet_generated_path)
common.log("INFO", "exec: " + cmd, conf)
if os.system(cmd) != 0:
error(action_error_msg + ' for run ' + run_id,
action_error_msg + '.\nCommand line:\n' + cmd, conf)
if not os.path.exists(input_samplesheet_generated_path):
error(action_error_msg + ' for run ' + run_id,
action_error_msg + ', the external command did not create Bcl2fastq CSV file:\n' + cmd, conf)
return None, None
# Load CSV samplesheet file
samplesheet = SampleSheetCSVReader(input_samplesheet_generated_path).read()
# Remove generated samplesheet
os.unlink(input_samplesheet_generated_path)
return samplesheet, None
else:
error('Error while creating Bcl2fastq CSV samplesheet file for run ' + run_id,
'No method to get Bcl2fastq samplesheet file has been defined. Please, set the ' +
'"bcl2fastq.samplesheet.format" property.\n',
conf)
return None, None
except AozanException, exp:
print StringUtils.stackTraceToString(exp)
error("Error reading samplesheet: " + samplesheet_filename, exp.getMessage(), conf)
return None, None
def sync(run_id, conf):
"""Synchronize a run.
Arguments:
run_id: the run id
conf: configuration dictionary
"""
start_time = time.time()
common.log('INFO', 'Sync step: Starting', conf)
bcl_data_path = conf[BCL_DATA_PATH_KEY]
reports_data_base_path = conf[REPORTS_DATA_PATH_KEY]
output_path = bcl_data_path + '/' + run_id
# check if rsync exists in PATH
if not common.exists_in_path("rsync"):
error("Can't find all needed commands in PATH env var",
"Can't find all needed commands in PATH env var. Unable to find: rsync command.", conf)
return False
# Check if reports_data_path exists
if not os.path.exists(reports_data_base_path):
error("Report directory does not exist", "Report directory does not exist: " + reports_data_base_path, conf)
return False
# Check if enough space to store reports
if common.df(reports_data_base_path) < 10 * 1024 * 1024 * 1024:
error("Not enough disk space to store aozan reports for run " + run_id,
"Not enough disk space to store aozan reports for run " + run_id +
'.\nNeed more than 10 Gb on ' + reports_data_base_path + '.', conf)
return False
# Do the synchronization
if not partial_sync(run_id, True, conf):
return False
# Rename partial sync directory to final run BCL directory
if os.path.exists(output_path + '.tmp'):
os.rename(output_path + '.tmp', output_path)
# Check used and free space
df_in_bytes = common.df(bcl_data_path)
du_in_bytes = common.du(output_path)
df = df_in_bytes / (1024 * 1024 * 1024)
du = du_in_bytes / (1024 * 1024 * 1024)
common.log("WARNING", "Sync step: output disk free after sync: " + str(df_in_bytes), conf)
common.log("WARNING", "Sync step: space used by sync: " + str(du_in_bytes), conf)
duration = time.time() - start_time
msg = 'Ending synchronization for run ' + run_id + '.\n' + \
'Job finished at ' + common.time_to_human_readable(time.time()) + \
' without error in ' + common.duration_to_human_readable(duration) + '.\n\n' + \
'Run output files (without .cif files) can be found in the following directory:\n ' + output_path
# Add path to report if reports.url exists
if common.is_conf_key_exists(REPORTS_URL_KEY, conf):
msg += '\n\nRun reports can be found at following location:\n ' + conf[REPORTS_URL_KEY] + '/' + run_id
msg += '\n\nFor this task %.2f GB has been used and %.2f GB is still free.' % (du, df)
common.send_msg('[Aozan] Ending synchronization for run ' + run_id + ' on ' +
common.get_instrument_name(run_id, conf), msg, False, conf)
common.log('INFO', 'sync step: successful in ' + common.duration_to_human_readable(duration), conf)
return True
qc.writeXMLReport(report, qc_output_dir + '/' + run_id + '.xml')
except AozanException, exp:
error("Error while computing QC XML report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
except Throwable, exp:
error("Error while computing QC XML report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
# Remove tmp extension of temporary QC directory
os.rename(qc_output_dir, qc_output_dir[:-len(tmp_extension)])
qc_output_dir = qc_output_dir[:-len(tmp_extension)]
# Write the HTML report
html_report_file = qc_output_dir + '/' + run_id + '.html'
try:
if not common.is_conf_key_exists(QC_REPORT_STYLESHEET_KEY, conf):
qc.writeReport(report, None, html_report_file)
else:
qc.writeReport(report, conf[QC_REPORT_STYLESHEET_KEY], html_report_file)
except AozanException, exp:
error("Error while computing QC HTML report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
except Throwable, exp:
error("error while computing QC HTML report for run " + run_id + ".", common.exception_msg(exp, conf), conf)
return False
# Check if the report has been generated
if not os.path.exists(html_report_file):
error("Error while computing QC report for run " + run_id + ".", "No HTML report generated", conf)
return False
