Commit a2cce4e7 authored by MARIJON Pierre's avatar MARIJON Pierre

fastq-dump failled apprently

parent 60a34183
......@@ -163,38 +163,38 @@ def finish(args):
def select(args):
for accession in args["input"]:
accession = accession.strip()
dump_call = ["fastq-dump", "-O"]
# accession = accession.strip()
# dump_call = ["fastq-dump", "-O"]
logging.info("begin of get information for "+accession)
# logging.info("begin of get information for "+accession)
data_path = args["data"] / accession
# build data directory
data_path.mkdir(parents=True, exist_ok=True)
run_id, assembly_len = get_info_about_ERS(accession)
if run_id is None and assembly_len is None:
logging.error("We didn't find assembly size for this species sorry we skip this !")
continue
logging.info("end of get information for "+accession)
# download file
logging.info("begin of download read for "+accession)
dump_call.append(os.path.abspath(str(data_path)))
dump_call.extend(run_id.split(" "))
logging.info(" ".join(dump_call))
logname = os.path.abspath(
str(args["data"] / accession / "fastq_dump_log"))
with open(logname+".out", "w") as outfile:
pass
out = subprocess.call(dump_call, stdout=outfile,
stderr=subprocess.STDOUT,
universal_newlines=True)
logging.info("end of download read for "+accession)
# # build data directory
# data_path.mkdir(parents=True, exist_ok=True)
# run_id, assembly_len = get_info_about_ERS(accession)
# if run_id is None and assembly_len is None:
# logging.error("We didn't find assembly size for this species sorry we skip this !")
# continue
# logging.info("end of get information for "+accession)
# # download file
# logging.info("begin of download read for "+accession)
# dump_call.append(os.path.abspath(str(data_path)))
# dump_call.extend(run_id.split(" "))
# logging.info(" ".join(dump_call))
# logname = os.path.abspath(
# str(args["data"] / accession / "fastq_dump_log"))
# with open(logname+".out", "w") as outfile:
# pass
# out = subprocess.call(dump_call, stdout=outfile,
# stderr=subprocess.STDOUT,
# universal_newlines=True)
# logging.info("end of download read for "+accession)
# compute coverage
logging.info("begin of compute canu parametre for "+accession)
......
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