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PengNi / ccsmeth

Detecting DNA methylation from PacBio CCS reads
BSD 3-Clause Clear License
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卡在11%不动了 #34

Closed rl4940 closed 1 year ago

rl4940 commented 1 year ago

你好！ 我做了call_mod 然后error_output给了下面这个：

split_holebatches process-19085 starts
extract_features process-19087 starts
[W::hts_idx_load3] The index file is older than the data file: /gpfs/data/pirontilab/Students/data/RobPacBio/121A/mapped.bam.bai
extract_features process-19095 starts
/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/torch/cuda/__init__.py:145: UserWarning: 
NVIDIA A100 80GB PCIe with CUDA capability sm_80 is not compatible with the current PyTorch installation.
The current PyTorch install supports CUDA capabilities sm_37 sm_50 sm_60 sm_61 sm_70 sm_75 compute_37.
If you want to use the NVIDIA A100 80GB PCIe GPU with PyTorch, please check the instructions at https://pytorch.org/get-started/locally/

  warnings.warn(incompatible_device_warn.format(device_name, capability, " ".join(arch_list), device_name))
extract_features process-19110 starts
/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/torch/cuda/__init__.py:145: UserWarning: 
NVIDIA A100 80GB PCIe with CUDA capability sm_80 is not compatible with the current PyTorch installation.
The current PyTorch install supports CUDA capabilities sm_37 sm_50 sm_60 sm_61 sm_70 sm_75 compute_37.
If you want to use the NVIDIA A100 80GB PCIe GPU with PyTorch, please check the instructions at https://pytorch.org/get-started/locally/

  warnings.warn(incompatible_device_warn.format(device_name, capability, " ".join(arch_list), device_name))
extract_features process-19144 starts
extract_features process-19152 starts
split_holebatches process-19085 generates 9340 hole/read batches(50)

batch_reader:   0%|          | 0/9340 [00:00<?, ?it/s][W::hts_idx_load3] The index file is older than the data file: /gpfs/data/pirontilab/Students/data/RobPacBio/121A/mapped.bam.bai
Process Process-8:
Process Process-5:

batch_reader:   0%|          | 10/9340 [00:00<11:41, 13.30it/s]Traceback (most recent call last):
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 531, in worker_extract_features_from_holebatches
    features_batch = _batch_feature_list2s(features_batch)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 480, in _batch_feature_list2s
    fipdms.append(np.array(kmer_ipdm, dtype=np.float))
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'float'.
`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
Traceback (most recent call last):
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 531, in worker_extract_features_from_holebatches
    features_batch = _batch_feature_list2s(features_batch)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 480, in _batch_feature_list2s
    fipdms.append(np.array(kmer_ipdm, dtype=np.float))
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'float'.
`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

batch_reader:   0%|          | 16/9340 [00:00<07:29, 20.76it/s]Process Process-3:
Process Process-9:
Process Process-7:
Traceback (most recent call last):
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 531, in worker_extract_features_from_holebatches
    features_batch = _batch_feature_list2s(features_batch)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 480, in _batch_feature_list2s
    fipdms.append(np.array(kmer_ipdm, dtype=np.float))
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'float'.
`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

batch_reader:   0%|          | 21/9340 [00:01<11:19, 13.71it/s]Traceback (most recent call last):
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 531, in worker_extract_features_from_holebatches
    features_batch = _batch_feature_list2s(features_batch)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 480, in _batch_feature_list2s
    fipdms.append(np.array(kmer_ipdm, dtype=np.float))
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'float'.
`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
Traceback (most recent call last):
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 531, in worker_extract_features_from_holebatches
    features_batch = _batch_feature_list2s(features_batch)
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/ccsmeth/extract_features.py", line 480, in _batch_feature_list2s
    fipdms.append(np.array(kmer_ipdm, dtype=np.float))
  File "/gpfs/data/pirontilab/Students/software/conda/envs/ccsmeth/lib/python3.10/site-packages/numpy/__init__.py", line 305, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'float'.
`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

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然后就一直在这里卡着，不知道咋办 感谢你

PengNi commented 1 year ago

你环境里的numpy版本是什么？可否换成1.22.4再试一下：

pip uninstall numpy
pip install numpy==1.22.4
rl4940 commented 1 year ago

你环境里的numpy版本是什么？可否换成1.22.4再试一下：

pip uninstall numpy
pip install numpy==1.22.4

哎woc，有道理，我试试，好像numpy报错了，感恩！