inq.empty(),
inq.qsize(),
inq.full(),
strftime("%Y-%m-%d %H:%M:%S"),
sum([reader.is_alive() for reader in readers]),
"q.size():",
q.qsize(),
file=sys.stderr,
sep="\t")
sys.stderr.flush()
sys.stdout.flush()
except Exception as e:
print(e, file=sys.stderr)
if args.top:
print("queue get timed out",
[reader.cpu_percent() for reader in reader_procs],
[worker.cpu_percent() for worker in worker_procs])
#print("#timed out",inq.empty())
print("#read from queue timed out:",
inq.empty(),
inq.qsize(),
inq.full(),
strftime("%Y-%m-%d %H:%M:%S"),
sum([reader.is_alive() for reader in readers]),
file=sys.stderr,
sep="\t")
sys.stderr.flush()
continue
if args.debug: print("got")
if not scaffold in pair_buffer:
pair_buffer[scaffold] = []
pair_buffer={}
scaffold_count={}
# while (not inq.empty()) or sum( [reader.is_alive() for reader in readers] )>0:
while True:
if args.debug: print("get")
try:
procid,scaffold,pairs = inq.get()
# procid,scaffold,pairs = inq.get(True,10)
#print("#got data:",procid,scaffold,len(pairs))
print("#got data from inq:",procid,scaffold,len(pairs),inq.empty(),inq.qsize(),inq.full(),strftime("%Y-%m-%d %H:%M:%S"),sum( [reader.is_alive() for reader in readers] ),"q.size():",q.qsize(),file=sys.stderr,sep="\t")
sys.stderr.flush()
sys.stdout.flush()
except Exception as e:
print(e,file=sys.stderr)
if args.top:
print("queue get timed out",[reader.cpu_percent() for reader in reader_procs],[worker.cpu_percent() for worker in worker_procs])
#print("#timed out",inq.empty())
print("#read from queue timed out:",inq.empty(),inq.qsize(),inq.full(),strftime("%Y-%m-%d %H:%M:%S"),sum( [reader.is_alive() for reader in readers] ),file=sys.stderr,sep="\t")
sys.stderr.flush()
continue
if args.debug: print("got")
if not scaffold in pair_buffer:
pair_buffer[scaffold]=[]
pair_buffer[scaffold] += pairs
scaffold_count[scaffold] = scaffold_count.get(scaffold,0)+1
# print("#:",scaffold,scaffold_count[scaffold])
if scaffold=="DONE":
print("#seen DONE {} times.".format(scaffold_count.get(scaffold,0)),strftime("%Y-%m-%d %H:%M:%S"),file=sys.stderr,sep="\t")
if scaffold_count[scaffold] == nbams:
print("#done. calling task_done:",strftime("%Y-%m-%d %H:%M:%S"),file=sys.stderr,sep="\t")
sys.stderr.flush()
