!export PYTHONPATH='C.Origami/src' && \
python C.Origami/src/corigami/inference/prediction.py \
--chr "chr10" \
--celltype "gm12878" \
--start 78000000 \
--model "./corigami_data/model_weights/corigami_base.ckpt" \
--seq "./corigami_data/data/hg38/dna_sequence" \
--ctcf "./corigami_data/data/hg38/gm12878/genomic_features/ctcf_log2fc.bw" \
--atac "./corigami_data/data/hg38/gm12878/genomic_features/atac.bw"
Reading sequence: ./corigami_data/data/hg38/dna_sequence/chr10.fa.gz
Feature path: ./corigami_data/data/hg38/gm12878/genomic_features/ctcf_log2fc.bw
Normalization status: None
Feature path: ./corigami_data/data/hg38/gm12878/genomic_features/atac.bw
Normalization status: log
Initializing ConvModel
Initializing ConvTransModel
Loading weights
Traceback (most recent call last):
File "/content/C.Origami/src/corigami/inference/prediction.py", line 42, in <module>
main()
File "/content/C.Origami/src/corigami/inference/prediction.py", line 27, in main
single_prediction(args.output_path, args.celltype,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/content/C.Origami/src/corigami/inference/prediction.py", line 35, in single_prediction
pred = infer.prediction(seq_region, ctcf_region, atac_region,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/content/C.Origami/src/corigami/inference/utils/inference_utils.py", line 53, in prediction
model = load_default(model_path)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/content/C.Origami/src/corigami/inference/utils/model_utils.py", line 12, in load_default
load_checkpoint(model, model_path)
File "/content/C.Origami/src/corigami/inference/utils/model_utils.py", line 25, in load_checkpoint
checkpoint = torch.load(model_path, map_location=device)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/dist-packages/torch/serialization.py", line 1529, in load
raise pickle.UnpicklingError(_get_wo_message(str(e))) from None
_pickle.UnpicklingError: Weights only load failed. This file can still be loaded, to do so you have two options, do those steps only if you trust the source of the checkpoint.
(1) In PyTorch 2.6, we changed the default value of the `weights_only` argument in `torch.load` from `False` to `True`. Re-running `torch.load` with `weights_only` set to `False` will likely succeed, but it can result in arbitrary code execution. Do it only if you got the file from a trusted source.
(2) Alternatively, to load with `weights_only=True` please check the recommended steps in the following error message.
WeightsUnpickler error: Unsupported global: GLOBAL omegaconf.dictconfig.DictConfig was not an allowed global by default. Please use `torch.serialization.add_safe_globals([omegaconf.dictconfig.DictConfig])` or the `torch.serialization.safe_globals([omegaconf.dictconfig.DictConfig])` context manager to allowlist this global if you trust this class/function.
File "/content/C.Origami/src/corigami/inference/utils/model_utils.py", line 25, in load_checkpoint
checkpoint = torch.load(model_path, map_location=device)
Code:
Error message:
Solution:
In this following line:
change to
checkpoint = torch.load(model_path, map_location=device, weights_only=False)