fibertools-rs 0.8.2

Fiber-seq toolkit in rust
Documentation 
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pytorch2.1.0:Ԗ
�
actual_input_1

conv_1.weight
conv_1.bias/conv_1/Conv_output_0/conv_1/Conv"Conv*
	dilations@�*
group�*
kernel_shape@�*
pads@@�*
strides@�2�/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/conv.py(294): _conv_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/conv.py(298): forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1039): _slow_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1051): _call_impl
/net/noble/vol4/noble/user/anupamaj/proj/m6A-calling/anupamaj/m6a_calling.py(173): forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1039): _slow_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1051): _call_impl
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/jit/_trace.py(952): trace_module
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/jit/_trace.py(735): trace
/tmp/ipykernel_63027/1181700565.py(3): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3441): run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3361): run_ast_nodes
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3169): run_cell_async
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/async_helpers.py(68): _pseudo_sync_runner
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2944): _run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2898): run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/zmqshell.py(533): run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/ipkernel.py(353): do_execute
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(648): execute_request
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(353): dispatch_shell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(446): process_one
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(457): dispatch_queue
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/events.py(81): _run
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(1859): _run_once
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(570): run_forever
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/tornado/platform/asyncio.py(199): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelapp.py(677): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/traitlets/config/application.py(846): launch_instance
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel_launcher.py(16): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(87): _run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(194): _run_module_as_main
Serialized   File "code/__torch__/torch/nn/modules/conv/___torch_mangle_108.py", line 11
    X: Tensor) -> Tensor:
    _0 = self.bias
    input = torch._convolution(X, self.weight, _0, [1], [0], [1], False, [0], 1, False, False, True, True)
            ~~~~~~~~~~~~~~~~~~ <--- HERE
    return input

�
/conv_1/Conv_output_0/Relu_output_0/Relu"Relu2�/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/functional.py(1298): relu
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/activation.py(102): forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1039): _slow_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1051): _call_impl
/net/noble/vol4/noble/user/anupamaj/proj/m6A-calling/anupamaj/m6a_calling.py(173): forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1039): _slow_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1051): _call_impl
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/jit/_trace.py(952): trace_module
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/jit/_trace.py(735): trace
/tmp/ipykernel_63027/1181700565.py(3): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3441): run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3361): run_ast_nodes
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3169): run_cell_async
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/async_helpers.py(68): _pseudo_sync_runner
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2944): _run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2898): run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/zmqshell.py(533): run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/ipkernel.py(353): do_execute
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(648): execute_request
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(353): dispatch_shell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(446): process_one
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(457): dispatch_queue
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/events.py(81): _run
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(1859): _run_once
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(570): run_forever
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/tornado/platform/asyncio.py(199): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelapp.py(677): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/traitlets/config/application.py(846): launch_instance
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel_launcher.py(16): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(87): _run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(194): _run_module_as_main
Serialized   File "code/__torch__/m6a_calling/___torch_mangle_114.py", line 18
    _2 = self.conv_3
    _3 = self.conv_2
    input = torch.relu((self.conv_1).forward(X, ))
            ~~~~~~~~~~ <--- HERE
    input0 = torch.relu((_3).forward(input, ))
    X0 = torch.relu((_2).forward(input0, ))

�
/Relu_output_0

conv_2.weight
conv_2.bias/conv_2/Conv_output_0/conv_2/Conv"Conv*
	dilations@�*
group�*
kernel_shape@�*
pads@@�*
strides@�2�/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/conv.py(294): _conv_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/conv.py(298): forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1039): _slow_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1051): _call_impl
/net/noble/vol4/noble/user/anupamaj/proj/m6A-calling/anupamaj/m6a_calling.py(174): forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1039): _slow_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1051): _call_impl
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/jit/_trace.py(952): trace_module
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/jit/_trace.py(735): trace
/tmp/ipykernel_63027/1181700565.py(3): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3441): run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3361): run_ast_nodes
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3169): run_cell_async
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/async_helpers.py(68): _pseudo_sync_runner
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2944): _run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2898): run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/zmqshell.py(533): run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/ipkernel.py(353): do_execute
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(648): execute_request
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(353): dispatch_shell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(446): process_one
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(457): dispatch_queue
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/events.py(81): _run
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(1859): _run_once
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(570): run_forever
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/tornado/platform/asyncio.py(199): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelapp.py(677): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/traitlets/config/application.py(846): launch_instance
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel_launcher.py(16): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(87): _run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(194): _run_module_as_main
Serialized   File "code/__torch__/torch/nn/modules/conv/___torch_mangle_109.py", line 11
    input: Tensor) -> Tensor:
    _0 = self.bias
    input0 = torch._convolution(input, self.weight, _0, [1], [0], [1], False, [0], 1, False, False, True, True)
             ~~~~~~~~~~~~~~~~~~ <--- HERE
    return input0

�
/conv_2/Conv_output_0/Relu_1_output_0/Relu_1"Relu2�/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/functional.py(1298): relu
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/activation.py(102): forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1039): _slow_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1051): _call_impl
/net/noble/vol4/noble/user/anupamaj/proj/m6A-calling/anupamaj/m6a_calling.py(174): forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1039): _slow_forward
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1051): _call_impl
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/jit/_trace.py(952): trace_module
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/jit/_trace.py(735): trace
/tmp/ipykernel_63027/1181700565.py(3): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3441): run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3361): run_ast_nodes
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3169): run_cell_async
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/async_helpers.py(68): _pseudo_sync_runner
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2944): _run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2898): run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/zmqshell.py(533): run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/ipkernel.py(353): do_execute
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(648): execute_request
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(353): dispatch_shell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(446): process_one
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelbase.py(457): dispatch_queue
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/events.py(81): _run
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(1859): _run_once
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(570): run_forever
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/tornado/platform/asyncio.py(199): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelapp.py(677): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/traitlets/config/application.py(846): launch_instance
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Serialized   File "code/__torch__/m6a_calling/___torch_mangle_114.py", line 19
    _3 = self.conv_2
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    input0 = torch.relu((_3).forward(input, ))
             ~~~~~~~~~~ <--- HERE
    X0 = torch.relu((_2).forward(input0, ))
    input1 = torch.flatten(X0, 1)

�
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Serialized   File "code/__torch__/torch/nn/modules/conv/___torch_mangle_110.py", line 11
    input: Tensor) -> Tensor:
    _0 = self.bias
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             ~~~~~~~~~~~~~~~~~~ <--- HERE
    return input0

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Serialized   File "code/__torch__/m6a_calling/___torch_mangle_114.py", line 20
    input = torch.relu((self.conv_1).forward(X, ))
    input0 = torch.relu((_3).forward(input, ))
    X0 = torch.relu((_2).forward(input0, ))
         ~~~~~~~~~~ <--- HERE
    input1 = torch.flatten(X0, 1)
    input2 = torch.relu((_1).forward(input1, ))

�
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Serialized   File "code/__torch__/m6a_calling/___torch_mangle_114.py", line 21
    input0 = torch.relu((_3).forward(input, ))
    X0 = torch.relu((_2).forward(input0, ))
    input1 = torch.flatten(X0, 1)
             ~~~~~~~~~~~~~ <--- HERE
    input2 = torch.relu((_1).forward(input1, ))
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�
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Serialized   File "code/__torch__/torch/nn/modules/linear/___torch_mangle_111.py", line 11
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             ~~~~~~~~~~~~ <--- HERE
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/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/traitlets/config/application.py(846): launch_instance
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/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(87): _run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(194): _run_module_as_main
Serialized   File "code/__torch__/m6a_calling/___torch_mangle_114.py", line 22
    X0 = torch.relu((_2).forward(input0, ))
    input1 = torch.flatten(X0, 1)
    input2 = torch.relu((_1).forward(input1, ))
             ~~~~~~~~~~ <--- HERE
    _4 = torch.softmax((_0).forward(input2, ), 1)
    return _4

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/tmp/ipykernel_63027/1181700565.py(3): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3441): run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3361): run_ast_nodes
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3169): run_cell_async
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/async_helpers.py(68): _pseudo_sync_runner
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2944): _run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2898): run_cell
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/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/events.py(81): _run
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(1859): _run_once
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(570): run_forever
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/tornado/platform/asyncio.py(199): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelapp.py(677): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/traitlets/config/application.py(846): launch_instance
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel_launcher.py(16): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(87): _run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(194): _run_module_as_main
Serialized   File "code/__torch__/torch/nn/modules/linear/___torch_mangle_112.py", line 11
    input: Tensor) -> Tensor:
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             ~~~~~~~~~~~~ <--- HERE
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�
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/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/torch/nn/modules/module.py(1039): _slow_forward
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/tmp/ipykernel_63027/1181700565.py(3): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3441): run_code
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3361): run_ast_nodes
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(3169): run_cell_async
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/async_helpers.py(68): _pseudo_sync_runner
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2944): _run_cell
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/IPython/core/interactiveshell.py(2898): run_cell
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/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/asyncio/base_events.py(570): run_forever
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/tornado/platform/asyncio.py(199): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel/kernelapp.py(677): start
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/traitlets/config/application.py(846): launch_instance
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/site-packages/ipykernel_launcher.py(16): <module>
/net/noble/vol1/home/anupamaj/miniconda3/lib/python3.8/runpy.py(87): _run_code
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Serialized   File "code/__torch__/m6a_calling/___torch_mangle_114.py", line 23
    input1 = torch.flatten(X0, 1)
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         ~~~~~~~~~~~~~ <--- HERE
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