Commit ed122dd6 authored by Rayan  CHIKHI's avatar Rayan CHIKHI
Browse files

tweaks

parent 6905947c
......@@ -39,8 +39,8 @@ def process_file(accession, region):
os.system(' '.join(["df", "-h","."]))
# some debug
public_sra_files = os.listdir(os.getcwd() + "/public/sra/")
print("at start, dir listing of public/sra/", public_sra_files)
print("at start, dir listing of /mnt/serratus-data")
os.system(' '.join(['ls','-alR','.']))
# download reads from accession
os.system('mkdir -p out/')
......@@ -53,6 +53,7 @@ def process_file(accession, region):
inputDataFn = accession+".inputdata.txt"
g = open(inputDataFn,"w")
for f in files:
print("file: " + f + " size: " + str(os.stat("out/"+f).st_size))
g.write(f + " " + str(os.stat("out/"+f).st_size)+"\n")
g.close()
......@@ -60,7 +61,7 @@ def process_file(accession, region):
# as per https://github.com/ababaian/serratus/blob/master/containers/serratus-dl/run_dl-sra.sh#L26
# run fastp
os.system(' '.join(["cat","out/*.fastq","|","/fastp", "--trim_poly_x", "--stdin", "-o", accession + ".fastq"]))
os.system(' '.join(["cat","out/*.fastq","|","/fastp", "--thread", "4", "--trim_poly_x", "--stdin", "-o", accession + ".fastq"]))
if os.stat(accession+".fastq").st_size == 0:
print("fastp produced empty output")
......
......@@ -138,7 +138,7 @@ Resources:
Type: SPOT
MinvCpus: 0
DesiredvCpus: 0
MaxvCpus: 1000
MaxvCpus: 4000
AllocationStrategy: SPOT_CAPACITY_OPTIMIZED
InstanceTypes:
- optimal
......
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