diff --git a/wort/blueprints/compute/tasks.py b/wort/blueprints/compute/tasks.py index 6ff3db1..abd29a8 100644 --- a/wort/blueprints/compute/tasks.py +++ b/wort/blueprints/compute/tasks.py @@ -56,8 +56,10 @@ def compute(sra_id): except CalledProcessError as e: if e.returncode == 3: # Happens when fastq-dump can't find an accession - # (might have been removed, redacted, or never uploaded) - pass + # (might have been removed, redacted, or never uploaded, + # and in some cases need dbGaP permission, like SRR27017016) + # stop further processing. + return # We ignore SIGPIPE, since it is informational (and makes sense, # it happens because `head` is closed and `fastq-dump` can't pipe @@ -65,6 +67,8 @@ def compute(sra_id): # http://www.pixelbeat.org/programming/sigpipe_handling.html elif e.returncode != 141: raise e + else: + result = result # if file is empty, consider it an error and sift # through logs later to figure out better error control