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-rw-r--r--bh20sequploader/qc_fasta.py2
1 files changed, 1 insertions, 1 deletions
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index 2600cfa..16cf2c9 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -46,7 +46,7 @@ def qc_fasta(sequence):
"-quicktree", "-iteration=none", "-type=DNA"]
print("QC checking similarity to reference")
print(" ".join(cmd))
- result = subprocess.run(cmd, capture_output=True)
+ result = subprocess.run(cmd, stdout=subprocess.PIPE)
res = result.stdout.decode("utf-8")
g1 = re.search(r"^Sequence 1: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE)
refbp = float(g1.group(1))