def analyze(analysis_object, config=None, config_file_path=None):
charon_session = CharonSession()
charon_pj=charon_session.project_get(analysis_object.project.project_id)
reference_genome=charon_pj.get('reference')
if charon_pj.get("sequencing_facility") == "NGI-S":
analysis_object.sequencing_facility="sthlm"
elif charon_pj.get("sequencing_facility") == "NGI-U":
analysis_object.sequencing_facility="upps"
else:
LOG.error("charon project not registered with stockholm or uppsala. Which config file should we use for the RNA pipeline ?")
raise RuntimeError
fastq_files=[]
if reference_genome and reference_genome != 'other':
for sample in analysis_object.project:
try:
charon_reported_status = charon_session.sample_get(analysis_object.project.project_id,
sample).get('analysis_status')
# Check Charon to ensure this hasn't already been processed
do_analyze=handle_sample_status(analysis_object, sample, charon_reported_status)
if not do_analyze :
continue
except CharonError as e:
LOG.error(e)
for libprep in sample:
charon_lp_status=charon_session.libprep_get(analysis_object.project.project_id, sample.name, libprep.name).get('qc')
do_analyze=handle_libprep_status(analysis_object, libprep, charon_lp_status)
if not do_analyze :
continue
else:
for seqrun in libprep:
charon_sr_status=charon_session.seqrun_get(analysis_object.project.project_id, sample.name, libprep.name, seqrun.name).get('alignment_status')
do_analyze=handle_seqrun_status(analysis_object, seqrun, charon_sr_status)
if not do_analyze :
continue
else:
seqrun.being_analyzed=True
sample.being_analyzed = sample.being_analyzed or True
# filter out index files from analysis
for fastq_file in filter(lambda f: not is_index_file(f), seqrun.fastq_files):
fastq_path=os.path.join(analysis_object.project.base_path, "DATA", analysis_object.project.project_id, sample.name, libprep.name, seqrun.name, fastq_file)
fastq_files.append(fastq_path)
if not fastq_files:
LOG.error("No fastq files obtained for the analysis fo project {}, please check the Charon status.".format(analysis_object.project.name))
else :
if analysis_object.restart_running_jobs:
stop_ongoing_analysis(analysis_object)
fastq_dir=preprocess_analysis(analysis_object, fastq_files)
sbatch_path=write_batch_job(analysis_object, reference_genome, fastq_dir)
job_id=start_analysis(sbatch_path)
analysis_path=os.path.join(analysis_object.project.base_path, "ANALYSIS", analysis_object.project.project_id, 'rna_ngi')
record_project_job(analysis_object.project, job_id, analysis_path)
def analyze(analysis_object,
level='sample',
config=None,
config_file_path=None):
"""Analyze data at the sample level.
:param NGIAnalysis analysis_object: holds all the parameters for the analysis
:raises ValueError: If exec_mode is an unsupported value
"""
charon_session = CharonSession()
for sample in analysis_object.project:
try:
charon_reported_status = charon_session.sample_get(
analysis_object.project.project_id,
sample).get('analysis_status')
# Check Charon to ensure this hasn't already been processed
do_analyze = handle_sample_status(analysis_object, sample,
charon_reported_status)
if not do_analyze:
continue
except CharonError as e:
LOG.error(e)
continue
if level == "sample":
status_field = "alignment_status"
elif level == "genotype":
status_field = "genotype_status"
else:
LOG.warn('Unknown workflow level: "{}"'.format(level))
status_field = "alignment_status" # Or should we abort?
try:
check_for_preexisting_sample_runs(
analysis_object.project, sample,
analysis_object.restart_running_jobs,
analysis_object.restart_finished_jobs, status_field)
except RuntimeError as e:
raise RuntimeError(
'Aborting processing of project/sample "{}/{}": '
'{}'.format(analysis_object.project, sample, e))
if analysis_object.exec_mode.lower() not in ("sbatch", "local"):
raise ValueError(
'"exec_mode" param must be one of "sbatch" or "local" '
'value was "{}"'.format(analysis_object.exec_mode))
if analysis_object.exec_mode == "local":
modules_to_load = analysis_object.config.get("piper", {}).get(
"load_modules", [])
load_modules(modules_to_load)
for workflow_subtask in workflows.get_subtasks_for_level(level=level):
if level == "genotype":
genotype_status = None # Some records in Charon lack this field, I'm guessing
try:
charon_session = CharonSession()
genotype_status = charon_session.sample_get(
projectid=analysis_object.project.project_id,
sampleid=sample.name).get("genotype_status")
except CharonError as e:
LOG.error(
'Couldn\'t determine genotyping status for project/'
'sample "{}/{}"; skipping analysis.'.format(
analysis_object.project, sample))
continue
if find_previous_genotype_analyses(
analysis_object.project,
sample) or genotype_status == "DONE":
if not analysis_object.restart_finished_jobs:
LOG.info(
'Project/sample "{}/{}" has completed genotype '
'analysis previously; skipping (use flag to force '
'analysis)'.format(analysis_object.project,
sample))
continue
if analysis_object.restart_running_jobs:
# Kill currently-running jobs if they exist
kill_running_sample_analysis(
workflow_subtask=workflow_subtask,
project_id=analysis_object.project.project_id,
sample_id=sample.name)
# This checks the local jobs database
if not is_sample_analysis_running_local(
workflow_subtask=workflow_subtask,
project_id=analysis_object.project.project_id,
sample_id=sample.name):
LOG.info('Launching "{}" analysis for sample "{}" in project '
'"{}"'.format(workflow_subtask, sample,
analysis_object.project))
try:
log_file_path = create_log_file_path(
workflow_subtask=workflow_subtask,
project_base_path=analysis_object.project.base_path,
project_name=analysis_object.project.dirname,
project_id=analysis_object.project.project_id,
sample_id=sample.name)
rotate_file(log_file_path)
exit_code_path = create_exit_code_file_path(
workflow_subtask=workflow_subtask,
project_base_path=analysis_object.project.base_path,
project_name=analysis_object.project.dirname,
project_id=analysis_object.project.project_id,
sample_id=sample.name)
if level == "sample":
if not analysis_object.keep_existing_data:
remove_previous_sample_analyses(
analysis_object.project, sample)
default_files_to_copy = None
elif level == "genotype":
if not analysis_object.keep_existing_data:
remove_previous_genotype_analyses(
analysis_object.project)
default_files_to_copy = None
# Update the project to keep only valid fastq files for setup.xml creation
if level == "genotype":
updated_project, default_files_to_copy = \
collect_files_for_sample_analysis(analysis_object.project,
sample,
restart_finished_jobs=True,
status_field="genotype_status")
else:
updated_project, default_files_to_copy = \
collect_files_for_sample_analysis(analysis_object.project,
sample,
analysis_object.restart_finished_jobs,
status_field="alignment_status")
setup_xml_cl, setup_xml_path = build_setup_xml(
project=updated_project,
sample=sample,
workflow=workflow_subtask,
local_scratch_mode=(
analysis_object.exec_mode == "sbatch"),
config=analysis_object.config)
piper_cl = build_piper_cl(
project=analysis_object.project,
workflow_name=workflow_subtask,
setup_xml_path=setup_xml_path,
exit_code_path=exit_code_path,
config=analysis_object.config,
exec_mode=analysis_object.exec_mode,
generate_bqsr_bam=analysis_object.generate_bqsr_bam)
if analysis_object.exec_mode == "sbatch":
process_id = None
slurm_job_id = sbatch_piper_sample(
[setup_xml_cl, piper_cl],
workflow_subtask,
analysis_object.project,
sample,
restart_finished_jobs=analysis_object.
restart_finished_jobs,
files_to_copy=default_files_to_copy)
for x in xrange(10):
# Time delay to let sbatch get its act together
# (takes a few seconds to be visible with sacct)
try:
get_slurm_job_status(slurm_job_id)
break
except ValueError:
time.sleep(2)
else:
LOG.error('sbatch file for sample {}/{} did not '
'queue properly! Job ID {} cannot be '
'found.'.format(analysis_object.project,
sample, slurm_job_id))
else: # "local"
raise NotImplementedError(
'Local execution not currently implemented. '
'I\'m sure Denis can help you with this.')
#slurm_job_id = None
#launch_piper_job(setup_xml_cl, project)
#process_handle = launch_piper_job(piper_cl, project)
#process_id = process_handle.pid
try:
record_process_sample(
project=analysis_object.project,
sample=sample,
analysis_module_name="piper_ngi",
slurm_job_id=slurm_job_id,
process_id=process_id,
workflow_subtask=workflow_subtask)
except RuntimeError as e:
LOG.error(e)
## Question: should we just kill the run in this case or let it go?
continue
except (NotImplementedError, RuntimeError, ValueError) as e:
error_msg = (
'Processing project "{}" / sample "{}" / workflow "{}" '
'failed: {}'.format(analysis_object.project, sample,
workflow_subtask, e))
LOG.error(error_msg)
def analyze(analysis_object, config=None, config_file_path=None):
charon_session = CharonSession()
charon_pj = charon_session.project_get(analysis_object.project.project_id)
reference_genome = charon_pj.get('reference')
if charon_pj.get("sequencing_facility") == "NGI-S":
analysis_object.sequencing_facility = "sthlm"
elif charon_pj.get("sequencing_facility") == "NGI-U":
analysis_object.sequencing_facility = "upps"
else:
LOG.error(
"charon project not registered with stockholm or uppsala. Which config file should we use for the RNA pipeline ?"
)
raise RuntimeError
fastq_files = []
if reference_genome and reference_genome != 'other':
for sample in analysis_object.project:
try:
charon_reported_status = charon_session.sample_get(
analysis_object.project.project_id,
sample).get('analysis_status')
# Check Charon to ensure this hasn't already been processed
do_analyze = handle_sample_status(analysis_object, sample,
charon_reported_status)
if not do_analyze:
continue
except CharonError as e:
LOG.error(e)
for libprep in sample:
charon_lp_status = charon_session.libprep_get(
analysis_object.project.project_id, sample.name,
libprep.name).get('qc')
do_analyze = handle_libprep_status(analysis_object, libprep,
charon_lp_status)
if not do_analyze:
continue
else:
for seqrun in libprep:
charon_sr_status = charon_session.seqrun_get(
analysis_object.project.project_id, sample.name,
libprep.name, seqrun.name).get('alignment_status')
do_analyze = handle_seqrun_status(
analysis_object, seqrun, charon_sr_status)
if not do_analyze:
continue
else:
seqrun.being_analyzed = True
sample.being_analyzed = sample.being_analyzed or True
for fastq_file in seqrun.fastq_files:
fastq_path = os.path.join(
analysis_object.project.base_path, "DATA",
analysis_object.project.project_id,
sample.name, libprep.name, seqrun.name,
fastq_file)
fastq_files.append(fastq_path)
if not fastq_files:
LOG.error(
"No fastq files obtained for the analysis fo project {}, please check the Charon status."
.format(analysis_object.project.name))
else:
if analysis_object.restart_running_jobs:
stop_ongoing_analysis(analysis_object)
fastq_dir = preprocess_analysis(analysis_object, fastq_files)
sbatch_path = write_batch_job(analysis_object, reference_genome,
fastq_dir)
job_id = start_analysis(sbatch_path)
analysis_path = os.path.join(analysis_object.project.base_path,
"ANALYSIS",
analysis_object.project.project_id,
'rna_ngi')
record_project_job(analysis_object.project, job_id, analysis_path)
def analyze(analysis_object, level='sample', config=None, config_file_path=None):
"""Analyze data at the sample level.
:param NGIAnalysis analysis_object: holds all the parameters for the analysis
:raises ValueError: If exec_mode is an unsupported value
"""
charon_session = CharonSession()
for sample in analysis_object.project:
try:
charon_reported_status = charon_session.sample_get(analysis_object.project.project_id,
sample).get('analysis_status')
# Check Charon to ensure this hasn't already been processed
do_analyze=handle_sample_status(analysis_object, sample, charon_reported_status)
if not do_analyze :
continue
except CharonError as e:
LOG.error(e)
continue
if level == "sample":
status_field = "alignment_status"
elif level == "genotype":
status_field = "genotype_status"
else:
LOG.warning('Unknown workflow level: "{}"'.format(level))
status_field = "alignment_status" # Or should we abort?
try:
check_for_preexisting_sample_runs(analysis_object.project, sample, analysis_object.restart_running_jobs,
analysis_object.restart_finished_jobs, status_field)
except RuntimeError as e:
raise RuntimeError('Aborting processing of project/sample "{}/{}": '
'{}'.format(analysis_object.project, sample, e))
if analysis_object.exec_mode.lower() not in ("sbatch", "local"):
raise ValueError('"exec_mode" param must be one of "sbatch" or "local" '
'value was "{}"'.format(analysis_object.exec_mode))
if analysis_object.exec_mode == "local":
modules_to_load = analysis_object.config.get("piper", {}).get("load_modules", [])
load_modules(modules_to_load)
for workflow_subtask in workflows.get_subtasks_for_level(level=level):
if level == "genotype":
genotype_status = None # Some records in Charon lack this field, I'm guessing
try:
charon_session = CharonSession()
genotype_status = charon_session.sample_get(projectid=analysis_object.project.project_id,
sampleid=sample.name).get("genotype_status")
except CharonError as e:
LOG.error('Couldn\'t determine genotyping status for project/'
'sample "{}/{}"; skipping analysis.'.format(analysis_object.project, sample))
continue
if find_previous_genotype_analyses(analysis_object.project, sample) or genotype_status == "DONE":
if not analysis_object.restart_finished_jobs:
LOG.info('Project/sample "{}/{}" has completed genotype '
'analysis previously; skipping (use flag to force '
'analysis)'.format(analysis_object.project, sample))
continue
if analysis_object.restart_running_jobs:
# Kill currently-running jobs if they exist
kill_running_sample_analysis(workflow_subtask=workflow_subtask,
project_id=analysis_object.project.project_id,
sample_id=sample.name)
# This checks the local jobs database
if not is_sample_analysis_running_local(workflow_subtask=workflow_subtask,
project_id=analysis_object.project.project_id,
sample_id=sample.name):
LOG.info('Launching "{}" analysis for sample "{}" in project '
'"{}"'.format(workflow_subtask, sample, analysis_object.project))
try:
log_file_path = create_log_file_path(workflow_subtask=workflow_subtask,
project_base_path=analysis_object.project.base_path,
project_name=analysis_object.project.dirname,
project_id=analysis_object.project.project_id,
sample_id=sample.name)
rotate_file(log_file_path)
exit_code_path = create_exit_code_file_path(workflow_subtask=workflow_subtask,
project_base_path=analysis_object.project.base_path,
project_name=analysis_object.project.dirname,
project_id=analysis_object.project.project_id,
sample_id=sample.name)
if level == "sample":
if not analysis_object.keep_existing_data:
remove_previous_sample_analyses(analysis_object.project, sample)
default_files_to_copy=None
elif level == "genotype":
if not analysis_object.keep_existing_data:
remove_previous_genotype_analyses(analysis_object.project)
default_files_to_copy=None
# Update the project to keep only valid fastq files for setup.xml creation
if level == "genotype":
updated_project, default_files_to_copy = \
collect_files_for_sample_analysis(analysis_object.project,
sample,
restart_finished_jobs=True,
status_field="genotype_status")
else:
updated_project, default_files_to_copy = \
collect_files_for_sample_analysis(analysis_object.project,
sample,
analysis_object.restart_finished_jobs,
status_field="alignment_status")
setup_xml_cl, setup_xml_path = build_setup_xml(project=updated_project,
sample=sample,
workflow=workflow_subtask,
local_scratch_mode=(analysis_object.exec_mode == "sbatch"),
config=analysis_object.config)
piper_cl = build_piper_cl(project=analysis_object.project,
workflow_name=workflow_subtask,
setup_xml_path=setup_xml_path,
exit_code_path=exit_code_path,
config=analysis_object.config,
exec_mode=analysis_object.exec_mode,
generate_bqsr_bam=analysis_object.generate_bqsr_bam)
if analysis_object.exec_mode == "sbatch":
process_id = None
slurm_job_id = sbatch_piper_sample([setup_xml_cl, piper_cl],
workflow_subtask,
analysis_object.project, sample,
restart_finished_jobs=analysis_object.restart_finished_jobs,
files_to_copy=default_files_to_copy)
for x in xrange(10):
# Time delay to let sbatch get its act together
# (takes a few seconds to be visible with sacct)
try:
get_slurm_job_status(slurm_job_id)
break
except ValueError:
time.sleep(2)
else:
LOG.error('sbatch file for sample {}/{} did not '
'queue properly! Job ID {} cannot be '
'found.'.format(analysis_object.project, sample, slurm_job_id))
else: # "local"
raise NotImplementedError('Local execution not currently implemented. '
'I\'m sure Denis can help you with this.')
#slurm_job_id = None
#launch_piper_job(setup_xml_cl, project)
#process_handle = launch_piper_job(piper_cl, project)
#process_id = process_handle.pid
try:
record_process_sample(project=analysis_object.project,
sample=sample,
analysis_module_name="piper_ngi",
slurm_job_id=slurm_job_id,
process_id=process_id,
workflow_subtask=workflow_subtask)
except RuntimeError as e:
LOG.error(e)
## Question: should we just kill the run in this case or let it go?
continue
except (NotImplementedError, RuntimeError, ValueError) as e:
error_msg = ('Processing project "{}" / sample "{}" / workflow "{}" '
'failed: {}'.format(analysis_object.project, sample,
workflow_subtask,
e))
LOG.error(error_msg)