Commit 6905947c authored by Rayan  CHIKHI's avatar Rayan CHIKHI
Browse files

oops, parallel-fastq-dump is maybe using /tmp

parent 896fc987
......@@ -45,7 +45,8 @@ def process_file(accession, region):
# download reads from accession
os.system('mkdir -p out/')
os.system('prefetch '+accession)
os.system('/parallel-fastq-dump --split-files --outdir out/ --threads 4 --sra-id '+accession)
os.system('mkdir -p tmp/')
os.system('/parallel-fastq-dump --split-files --outdir out/ --tmpdir tmp/ --threads 4 --sra-id '+accession)
files = os.listdir(os.getcwd() + "/out/")
print("after fastq-dump, dir listing of out/", files)
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