Hello, I encountered an error while trying to construct a network using TkNA. I ran the following command in the terminal on my MacBook Pro:python ../reconstruction/run.py --data-source ./test_AB.zip --config-file ./config.json --out-file ./network_output.zipUnfortunately, I received the following error message:
Traceback (most recent call last):
File "../reconstruction/run.py", line 66, in
network_reconstructor.reconstructNetwork(config, dataset, start=args.start, stopStage=args.stop, dataOutFilePath=args.outFile, cores=args.cores)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 749, in reconstructNetwork
return self.runPipeline(stages, allData, *kwargs)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructor.py", line 59, in runPipeline
stage(allData)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 695, in computeCorrelations
allData["correlationCoefficients"], allData["correlationPValues"] = calculateCorrelations(config, allData["filteredData"], cores)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 463, in calculateCorrelations
correlationResults = treatmentData.groupby("metatreatment").map(calculateForMetatreatment)
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/site-packages/xarray/core/groupby.py", line 795, in map
return self._combine(applied, shortcut=shortcut)
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/site-packages/xarray/core/groupby.py", line 814, in _combine
applied_example, applied = peek_at(applied)
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/site-packages/xarray/core/utils.py", line 196, in peek_at
peek = next(gen)
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/site-packages/xarray/core/groupby.py", line 794, in
applied = (maybe_wrap_array(arr, func(arr, args, **kwargs)) for arr in grouped)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 423, in calculateForMetatreatment
treatmentDataSharedMemory = shared_memory.SharedMemory(create=True, size=treatmentData.nbytes, name=sharedMemoryName("treatmentData", runnerId))
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/multiprocessing/shared_memory.py", line 102, in init
self._fd = _posixshmem.shm_open(
OSError: [Errno 63] File name too long: '/treatmentData_1712824020.879668'
(tkna) XinyuedeMacBook-Pro:input xinyuezhu$ /Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 2 leaked shared_memory objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '
It appears that the error is due to the filename exceeding the maximum length allowed by the system. Could you please advise me on how to address this issue? Any assistance would be greatly appreciated. Thank you!
Hello, I encountered an error while trying to construct a network using TkNA. I ran the following command in the terminal on my MacBook Pro:
network_reconstructor.reconstructNetwork(config, dataset, start=args.start, stopStage=args.stop, dataOutFilePath=args.outFile, cores=args.cores)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 749, in reconstructNetwork
return self.runPipeline(stages, allData, *kwargs)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructor.py", line 59, in runPipeline
stage(allData)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 695, in computeCorrelations
allData["correlationCoefficients"], allData["correlationPValues"] = calculateCorrelations(config, allData["filteredData"], cores)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 463, in calculateCorrelations
correlationResults = treatmentData.groupby("metatreatment").map(calculateForMetatreatment)
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/site-packages/xarray/core/groupby.py", line 795, in map
return self._combine(applied, shortcut=shortcut)
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/site-packages/xarray/core/groupby.py", line 814, in _combine
applied_example, applied = peek_at(applied)
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/site-packages/xarray/core/utils.py", line 196, in peek_at
peek = next(gen)
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/site-packages/xarray/core/groupby.py", line 794, in
applied = (maybe_wrap_array(arr, func(arr, args, **kwargs)) for arr in grouped)
File "/Users/xinyuezhu/Work/Benchmark causal inference method/test_method/TkNA-main/reconstruction/reconstruction/NetworkReconstructorAggregate.py", line 423, in calculateForMetatreatment
treatmentDataSharedMemory = shared_memory.SharedMemory(create=True, size=treatmentData.nbytes, name=sharedMemoryName("treatmentData", runnerId))
File "/Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/multiprocessing/shared_memory.py", line 102, in init
self._fd = _posixshmem.shm_open(
OSError: [Errno 63] File name too long: '/treatmentData_1712824020.879668'
(tkna) XinyuedeMacBook-Pro:input xinyuezhu$ /Users/xinyuezhu/opt/anaconda3/envs/tkna/lib/python3.8/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 2 leaked shared_memory objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '
python ../reconstruction/run.py --data-source ./test_AB.zip --config-file ./config.json --out-file ./network_output.zipUnfortunately, I received the following error message: Traceback (most recent call last): File "../reconstruction/run.py", line 66, inIt appears that the error is due to the filename exceeding the maximum length allowed by the system. Could you please advise me on how to address this issue? Any assistance would be greatly appreciated. Thank you!