Commit 262e1ba3 authored by Rayan  CHIKHI's avatar Rayan CHIKHI
Browse files

apparently docker doesnt like my args

parent bbd3cdb7
......@@ -79,12 +79,12 @@ def process_file(accession, region):
prefetch_start = datetime.now()
# 'is larger than maximum allowed: skipped' solved by:
# https://wiki.rc.hms.harvard.edu/display/O2/Aspera+to+download+NCBI+SRA+data
os.system('prefetch --max-size 35G '+accession)
os.system('prefetch -X 35G '+accession)
prefetch_time = datetime.now() - prefetch_start
sdb_log(sdb,accession,'prefetch_time',int(prefetch_time.seconds))
os.system('mkdir -p tmp/')
pfqdump_start = datetime.now()
os.system('/parallel-fastq-dump --skip-technical --split-3 --outdir out/ --tmpdir tmp/ --threads 4 --sra-id '+accession)
os.system('/parallel-fastq-dump --skip-technical --split-e --outdir out/ --tmpdir tmp/ --threads 4 --sra-id '+accession)
pfqdump_time = datetime.now() - pfqdump_start
sdb_log(sdb,accession,'pfqdump_time',int(pfqdump_time.seconds))
......
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