Open jiuhai opened 1 year ago
Sorry for my late response.
Thank you very much for reporting the error.
I actually found an error related to multiprocessing on Mac which I could not observe in Linux. I'm not sure if this error is relevant to your error, but I have already fixed this bug and have released as v2.2.4. Therefore, if you have an opportunity, please try test dataset with new version.
Best regards, Yu
I got an error like this and it stopped.
[QTL-seq:2023-07-17 23:05:13] start to run QTL-seq. [QTL-seq:2023-07-17 23:05:13] maximum number of threads which you can use is up to 16. [QTL-seq:2023-07-17 23:05:13] start to index reference fasta. [QTL-seq:2023-07-17 23:05:14] indexing of reference successfully finished. [QTL-seq:2023-07-17 23:05:14] start to align reads of parent.0000 by BWA. [QTL-seq:2023-07-17 23:05:19] alignment parent.0000 successfully finished. [QTL-seq:2023-07-17 23:05:19] start to align reads of bulk1.0000 by BWA. [QTL-seq:2023-07-17 23:05:23] alignment bulk1.0000 successfully finished. [QTL-seq:2023-07-17 23:05:23] start to align reads of bulk2.0000 by BWA. [QTL-seq:2023-07-17 23:05:28] alignment bulk2.0000 successfully finished. [QTL-seq:2023-07-17 23:05:28] start to merge BAMs. [QTL-seq:2023-07-17 23:05:30] merging process successfully finished. [QTL-seq:2023-07-17 23:05:30] start to call variants. Process SpawnPoolWorker-2: Traceback (most recent call last): File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, self._kwargs) File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/pool.py", line 114, in worker task = get() File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/queues.py", line 367, in get return _ForkingPickler.loads(res) File "/Users/jiuhaizhao/Documents/QTLseq/QTL-seq/qtlseq/mpileup.py", line 7, in
from qtlseq.vcf2index import Vcf2Index
File "/Users/jiuhaizhao/Documents/QTLseq/QTL-seq/qtlseq/vcf2index.py", line 10, in
cache = Manager().dict()
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/context.py", line 57, in Manager
m.start()
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/managers.py", line 554, in start
self._process.start()
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/process.py", line 118, in start
assert not _current_process._config.get('daemon'), \
AssertionError: daemonic processes are not allowed to have children
^CProcess SpawnPoolWorker-4:
Process SpawnPoolWorker-3:
Traceback (most recent call last):
File "/Users/jiuhaizhao/miniconda3/bin/qtlseq", line 33, in
sys.exit(load_entry_point('qtlseq', 'console_scripts', 'qtlseq')())
File "/Users/jiuhaizhao/Documents/QTLseq/QTL-seq/qtlseq/qtlseq.py", line 171, in main
Traceback (most recent call last):
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, *self._kwargs)
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/queues.py", line 364, in get
with self._rlock:
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/synchronize.py", line 95, in enter
return self._semlock.enter()
Traceback (most recent call last):
KeyboardInterrupt
QTLseq(args).run()
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/Users/jiuhaizhao/Documents/QTLseq/QTL-seq/qtlseq/qtlseq.py", line 166, in run
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(self._args, self._kwargs)
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/pool.py", line 114, in worker
task = get()
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/queues.py", line 365, in get
res = self._reader.recv_bytes()
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/connection.py", line 221, in recv_bytes
buf = self._recv_bytes(maxlength)
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/connection.py", line 419, in _recv_bytes
buf = self._recv(4)
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/connection.py", line 384, in _recv
chunk = read(handle, remaining)
KeyboardInterrupt
self.mpileup()
File "/Users/jiuhaizhao/Documents/QTLseq/QTL-seq/qtlseq/qtlseq.py", line 122, in mpileup
mp.run()
File "/Users/jiuhaizhao/Documents/QTLseq/QTL-seq/qtlseq/mpileup.py", line 228, in run
p.map(self.mpileup, chr_names)
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/pool.py", line 765, in get
self.wait(timeout)
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/multiprocessing/pool.py", line 762, in wait
self._event.wait(timeout)
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/threading.py", line 581, in wait
signaled = self._cond.wait(timeout)
File "/Users/jiuhaizhao/miniconda3/lib/python3.9/threading.py", line 312, in wait
waiter.acquire()
KeyboardInterrupt