Can not get_cns

[shehongbing]

HI,

During the get_cns step, it spend a few days but can not get the cns.fasta. And I run it again but it also can not get the cns.fasta. So I run the script nextDenovo.sh, and there is some errors:

hostname

• hostname mu01 cd /data/pub/shehb/ONT/nextdenovo/raw_xx_change/raw_n01_newparameter/02.cns_align/01.get_cns.sh.work/get_cns00
• cd /data/pub/shehb/ONT/nextdenovo/raw_xx_change/raw_n01_newparameter/02.cns_align/01.get_cns.sh.work/get_cns00 time python /data/pub/shehb/soft/NextDenovo/lib/nextcorrect.py -f /data/pub/shehb/ONT/nextdenovo/raw_xx_change/raw_n01_newparameter/02.cns_align//01.get_cns.input.idxs -i /data/pub/shehb/ONT/nextdenovo/raw_xx_change/raw_n01_newparameter/01.raw_align/03.sort_align.sh.work/sort_align00/input.seed.017.sorted.ovl -p 15 -b -max_lq_length 10000 -o cns.fasta;
• python /data/pub/shehb/soft/NextDenovo/lib/nextcorrect.py -f /data/pub/shehb/ONT/nextdenovo/raw_xx_change/raw_n01_newparameter/02.cns_align//01.get_cns.input.idxs -i /data/pub/shehb/ONT/nextdenovo/raw_xx_change/raw_n01_newparameter/01.raw_align/03.sort_align.sh.work/sort_align00/input.seed.017.sorted.ovl -p 15 -b -max_lq_length 10000 -o cns.fasta [INFO] 2020-02-21 10:22:33,976 Corrected step options: [INFO] 2020-02-21 10:22:33,977 Namespace(blacklist=False, dbuf=False, fast=False, idxs='/data/pub/shehb/ONT/nextdenovo/raw_xx_change/raw_n01_newparameter/02.cns_align//01.get_cns.input.idxs', max_cov_aln=130, max_lq_length=10000, min_cov_base=4, min_cov_seed=10, min_error_corrected_ratio=0.8, min_len_aln=500, min_len_seed=10000, out='cns.fasta', ovl='/data/pub/shehb/ONT/nextdenovo/raw_xx_change/raw_n01_newparameter/01.raw_align/03.sort_align.sh.work/sort_align00/input.seed.017.sorted.ovl', process=15, split=False) Traceback (most recent call last): File "/data/pub/shehb/soft/NextDenovo/lib/nextcorrect.py", line 304, in main(args) File "/data/pub/shehb/soft/NextDenovo/lib/nextcorrect.py", line 224, in main pool = Pool(args.process, initializer=start) File "/usr/lib64/python2.7/multiprocessing/init.py", line 232, in Pool return Pool(processes, initializer, initargs, maxtasksperchild) File "/usr/lib64/python2.7/multiprocessing/pool.py", line 138, in init self._setup_queues() File "/usr/lib64/python2.7/multiprocessing/pool.py", line 233, in _setup_queues self._inqueue = SimpleQueue() File "/usr/lib64/python2.7/multiprocessing/queues.py", line 352, in init self._rlock = Lock() File "/usr/lib64/python2.7/multiprocessing/synchronize.py", line 147, in init SemLock.init(self, SEMAPHORE, 1, 1) File "/usr/lib64/python2.7/multiprocessing/synchronize.py", line 75, in init sl = self._semlock = _multiprocessing.SemLock(kind, value, maxvalue) OSError: [Errno 13] Permission denied

could you please give me some advices THX

[moold]

It is a system configuration problem, see here and ask your system administrator for help.

[shehongbing]

Thank you

在 2020年2月21日，上午10:39，Hu Jiang notifications@github.com 写道：

It is a system configuration problem, see here https://stackoverflow.com/questions/2009278/python-multiprocessing-permission-denied and ask your system administrator for help.

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