xunchen85
commented
8 months ago I have resolved it by changing to use another computer.
Xun
Closed xunchen85 closed 8 months ago
xunchen85
commented
8 months ago I have resolved it by changing to use another computer.
Xun
Dear XiaoTao,
I was able to use it to generate the assemblie file, although I got the following errors when I called the neo-loops. I have attached the log files below. I am wondering if you could kindly help!
Best wishes, Xun
log file
ARGUMENT LIST:
Output Path = Tong_inter_30.2.eagle.neoloops.txt
Cache Folder = .cache
SV assembly = Tong_inter_30.2.eagle.assemblies.txt
Cooler List = ['Tong_inter_30.2.mcool::resolutions/50000', 'Tong_inter_30.2.mcool::resolutions/10000', 'Tong_inter_30.2.mcool::resolutions/5000']
Extended Genomic Span = 3000000bp
Balance Type = CNV
Probability threshold = 0.95
No pooling = False
Minimum marginal peaks = 2
Number of Processes = 4
Log file name = Tong_inter_30.2.eagle.neoloops.log
numexpr.utils INFO @ 10/12/23 22:28:42: Note: NumExpr detected 40 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. numexpr.utils INFO @ 10/12/23 22:28:42: NumExpr defaulting to 8 threads. root INFO @ 10/12/23 22:28:52: Load assembled SVs root INFO @ 10/12/23 22:28:52: Current resolution: 50000 root INFO @ 10/12/23 22:28:52: Calculate the global average contact frequencies at each genomic distance ... root INFO @ 10/12/23 22:28:57: Done joblib.externals.loky.process_executor._RemoteTraceback: """ Traceback (most recent call last): File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/externals/loky/process_executor.py", line 428, in _process_worker r = call_item() File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/externals/loky/process_executor.py", line 275, in call return self.fn(*self.args, self.kwargs) File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/_parallel_backends.py", line 620, in call return self.func(*args, *kwargs) File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/parallel.py", line 288, in call return [func(args, kwargs) File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/parallel.py", line 288, in
return [func(*args, **kwargs)
File "/home/xchen85/ENV3.8_fanc/bin/neoloop-caller", line 202, in pipeline
core.load_models(models_by_res[fu.res])
File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/neoloop/callers.py", line 576, in load_models
self.model = joblib.load(model_fil_path)
File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 658, in load
obj = _unpickle(fobj, filename, mmap_mode)
File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 577, in _unpickle
obj = unpickler.load()
File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/lib/python3.8/pickle.py", line 1210, in load
raise EOFError
EOFError
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/xchen85/ENV3.8_fanc/bin/neoloop-caller", line 157, in run results = Parallel(n_jobs=args.nproc, verbose=10)(delayed(pipeline)(*i) for i in Params) File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/parallel.py", line 1098, in call self.retrieve() File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/parallel.py", line 975, in retrieve self._output.extend(job.get(timeout=self.timeout)) File "/home/xchen85/ENV3.8_fanc/lib/python3.8/site-packages/joblib/_parallel_backends.py", line 567, in wrap_future_result return future.result(timeout=timeout) File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/lib/python3.8/concurrent/futures/_base.py", line 444, in result return self.get_result() File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Core/python/3.8.10/lib/python3.8/concurrent/futures/_base.py", line 389, in get_result raise self._exception EOFError