TFs perturbation prediction with RegVelo#
Library imports#
import shutil
import numpy as np
import pandas as pd
import torch
import scanpy as sc
import scvi
from regvelo import REGVELOVI
from rgv_tools import DATA_DIR, FIG_DIR
from rgv_tools.perturbation import get_list_name, TFScanning
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_excel from `anndata` is deprecated. Import anndata.io.read_excel instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_mtx from `anndata` is deprecated. Import anndata.io.read_mtx instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_hdf from `anndata` is deprecated. Import anndata.io.read_hdf instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_umi_tools from `anndata` is deprecated. Import anndata.io.read_umi_tools instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing CSCDataset from `anndata.experimental` is deprecated. Import anndata.abc.CSCDataset instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing CSRDataset from `anndata.experimental` is deprecated. Import anndata.abc.CSRDataset instead.
warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/dynamo/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_elem from `anndata.experimental` is deprecated. Import anndata.io.read_elem instead.
warnings.warn(msg, FutureWarning)
General settings#
scvi.settings.seed = 0
[rank: 0] Seed set to 0
Constants#
DATASET = "zebrafish"
SAVE_DATA = True
if SAVE_DATA:
(DATA_DIR / DATASET / "processed").mkdir(parents=True, exist_ok=True)
(DATA_DIR / DATASET / "results").mkdir(parents=True, exist_ok=True)
SAVE_FIGURES = True
if SAVE_FIGURES:
(FIG_DIR / DATASET).mkdir(parents=True, exist_ok=True)
TERMINAL_STATES = [
"mNC_head_mesenchymal",
"mNC_arch2",
"mNC_hox34",
"Pigment",
]
Data Loading#
adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed.h5ad")
Perturbation screening#
## prepare skeleton
W = adata.uns["skeleton"].copy()
W = torch.tensor(np.array(W)).int()
## prepare TF
TF = adata.var_names[adata.var["TF"]]
### repeat run the model to get aggregate performance
for nrun in range(3):
print("training model...")
REGVELOVI.setup_anndata(adata, spliced_layer="Ms", unspliced_layer="Mu")
vae = REGVELOVI(adata, W=W.T, regulators=TF, soft_constraint=False)
torch.cuda.empty_cache()
vae.train()
print("save model...")
model_name = "rgv_model_" + str(nrun)
coef_name = "coef_" + str(nrun)
pval_name = "pval_" + str(nrun)
model = DATA_DIR / DATASET / "processed" / "perturb_repeat_runs" / model_name
coef_save = DATA_DIR / DATASET / "results" / coef_name
pval_save = DATA_DIR / DATASET / "results" / pval_name
vae.save(model)
print("inferring perturbation...")
# TODO: Add concrete Error to except clause
while True:
try:
perturb_screening = TFScanning(model, adata, 7, "cell_type", TERMINAL_STATES, TF, 0)
coef = pd.DataFrame(np.array(perturb_screening["coefficient"]))
coef.index = perturb_screening["TF"]
coef.columns = get_list_name(perturb_screening["coefficient"][0])
pval = pd.DataFrame(np.array(perturb_screening["pvalue"]))
pval.index = perturb_screening["TF"]
pval.columns = get_list_name(perturb_screening["pvalue"][0])
rows_with_nan = coef.isna().any(axis=1)
# Set all values in those rows to NaN
coef.loc[rows_with_nan, :] = np.nan
pval.loc[rows_with_nan, :] = np.nan
coef.to_csv(coef_save)
pval.to_csv(pval_save)
break
except: # noqa E722
# If an error is raised, increment a and try again, and need to recompute double knock-out reults
print("perturbation screening has error, retraining model...")
shutil.rmtree(model)
REGVELOVI.setup_anndata(adata, spliced_layer="Ms", unspliced_layer="Mu")
vae = REGVELOVI(adata, W=W.T, regulators=TF, soft_constraint=False)
vae.train()
print("save model...")
vae.save(model)
training model...
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
You are using a CUDA device ('NVIDIA A100-PCIE-40GB MIG 3g.20gb') that has Tensor Cores. To properly utilize them, you should set `torch.set_float32_matmul_precision('medium' | 'high')` which will trade-off precision for performance. For more details, read https://pytorch.org/docs/stable/generated/torch.set_float32_matmul_precision.html#torch.set_float32_matmul_precision
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [MIG-7294bf77-f0a0-562e-86ad-a0b5c0de66d3]
Monitored metric elbo_validation did not improve in the last 45 records. Best score: -2379.619. Signaling Trainer to stop.
save model...
inferring perturbation...
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:55:38,995 - INFO - Using pre-computed Schur decomposition
WARNING: Unable to import petsc4py. For installation, please refer to: https://petsc4py.readthedocs.io/en/stable/install.html.
Defaulting to `'gmres'` solver.
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:55:49,583 - INFO - Using pre-computed Schur decomposition
Done alx4a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:55:59,846 - INFO - Using pre-computed Schur decomposition
Done arntl1b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:56:09,983 - INFO - Using pre-computed Schur decomposition
Done bach2b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:56:20,209 - INFO - Using pre-computed Schur decomposition
Done bhlhe40
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:56:30,742 - INFO - Using pre-computed Schur decomposition
Done bhlhe41
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:56:41,030 - INFO - Using pre-computed Schur decomposition
Done dlx1a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:56:51,993 - INFO - Using pre-computed Schur decomposition
Done ebf1b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:57:02,395 - INFO - Using pre-computed Schur decomposition
Done ebf3a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:57:12,736 - INFO - Using pre-computed Schur decomposition
Done egr1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:57:23,282 - INFO - Using pre-computed Schur decomposition
Done egr2b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:57:34,149 - INFO - Using pre-computed Schur decomposition
Done egr3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:57:44,399 - INFO - Using pre-computed Schur decomposition
Done egr4
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:57:54,828 - INFO - Using pre-computed Schur decomposition
Done elf1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:58:05,261 - INFO - Using pre-computed Schur decomposition
Done elk3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:58:15,627 - INFO - Using pre-computed Schur decomposition
Done erf
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:58:25,876 - INFO - Using pre-computed Schur decomposition
Done erfl3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:58:36,233 - INFO - Using pre-computed Schur decomposition
Done ets1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:58:46,830 - INFO - Using pre-computed Schur decomposition
Done etv5b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:58:57,556 - INFO - Using pre-computed Schur decomposition
Done fli1a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:59:08,091 - INFO - Using pre-computed Schur decomposition
Done fosab
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:59:18,822 - INFO - Using pre-computed Schur decomposition
Done fosl1a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:59:29,442 - INFO - Using pre-computed Schur decomposition
Done fosl2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:59:39,952 - INFO - Using pre-computed Schur decomposition
Done her9
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 12:59:50,652 - INFO - Using pre-computed Schur decomposition
Done hnf1ba
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:00:01,088 - INFO - Using pre-computed Schur decomposition
Done hnf1bb
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:00:11,825 - INFO - Using pre-computed Schur decomposition
Done hoxa11b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:00:22,992 - INFO - Using pre-computed Schur decomposition
Done hoxa2b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:00:33,579 - INFO - Using pre-computed Schur decomposition
Done hoxa4a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:00:43,986 - INFO - Using pre-computed Schur decomposition
Done hoxa9a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:00:55,014 - INFO - Using pre-computed Schur decomposition
Done hoxa9b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:01:05,415 - INFO - Using pre-computed Schur decomposition
Done hoxb10a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:01:16,129 - INFO - Using pre-computed Schur decomposition
Done hoxb1b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:01:26,552 - INFO - Using pre-computed Schur decomposition
Done hoxb5b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:01:37,565 - INFO - Using pre-computed Schur decomposition
Done hoxb9a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:01:48,153 - INFO - Using pre-computed Schur decomposition
Done hoxc11b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:01:58,954 - INFO - Using pre-computed Schur decomposition
Done hoxc3a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:02:09,693 - INFO - Using pre-computed Schur decomposition
Done hoxc9a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:02:20,438 - INFO - Using pre-computed Schur decomposition
Done hoxd11a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:02:31,199 - INFO - Using pre-computed Schur decomposition
Done hoxd12a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:02:41,661 - INFO - Using pre-computed Schur decomposition
Done jdp2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:02:52,603 - INFO - Using pre-computed Schur decomposition
Done jun
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:03:05,220 - INFO - Using pre-computed Schur decomposition
Done junba
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:03:16,341 - INFO - Using pre-computed Schur decomposition
Done mitfa
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:03:27,602 - INFO - Using pre-computed Schur decomposition
Done msx1b
INFO File
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el.pt already downloaded
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2024-11-24 13:03:38,352 - INFO - Using pre-computed Schur decomposition
Done msx3
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:03:49,249 - INFO - Using pre-computed Schur decomposition
Done mycb
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:04:00,337 - INFO - Using pre-computed Schur decomposition
Done nfe2l2a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:04:11,191 - INFO - Using pre-computed Schur decomposition
Done nr2f2
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:04:22,751 - INFO - Using pre-computed Schur decomposition
Done nr2f5
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:04:33,661 - INFO - Using pre-computed Schur decomposition
Done nr2f6b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:04:44,624 - INFO - Using pre-computed Schur decomposition
Done nr4a2b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:04:55,279 - INFO - Using pre-computed Schur decomposition
Done nr4a3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
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2024-11-24 13:05:06,396 - INFO - Using pre-computed Schur decomposition
Done otx2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:05:17,737 - INFO - Using pre-computed Schur decomposition
Done pbx1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:05:28,895 - INFO - Using pre-computed Schur decomposition
Done pknox2
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:05:39,831 - INFO - Using pre-computed Schur decomposition
Done rarga
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:05:50,818 - INFO - Using pre-computed Schur decomposition
Done rxraa
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:06:01,811 - INFO - Using pre-computed Schur decomposition
Done snai1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:06:12,526 - INFO - Using pre-computed Schur decomposition
Done sox10
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:06:23,242 - INFO - Using pre-computed Schur decomposition
Done sox6
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:06:33,890 - INFO - Using pre-computed Schur decomposition
Done sox9b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:06:44,790 - INFO - Using pre-computed Schur decomposition
Done tead1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:06:56,171 - INFO - Using pre-computed Schur decomposition
Done tead1b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:07:07,117 - INFO - Using pre-computed Schur decomposition
Done tead3a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:07:18,118 - INFO - Using pre-computed Schur decomposition
Done tead3b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:07:29,412 - INFO - Using pre-computed Schur decomposition
Done tfap2a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:07:40,455 - INFO - Using pre-computed Schur decomposition
Done tfap2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:07:51,251 - INFO - Using pre-computed Schur decomposition
Done tfap2e
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:08:02,411 - INFO - Using pre-computed Schur decomposition
Done tfeb
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:08:13,191 - INFO - Using pre-computed Schur decomposition
Done tfec
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:08:24,314 - INFO - Using pre-computed Schur decomposition
Done twist1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:08:34,941 - INFO - Using pre-computed Schur decomposition
Done twist1b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:08:46,256 - INFO - Using pre-computed Schur decomposition
Done zeb1b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
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WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:08:57,157 - INFO - Using pre-computed Schur decomposition
Done zic2a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_0/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:09:08,312 - INFO - Using pre-computed Schur decomposition
Done zic2b
training model...
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [MIG-7294bf77-f0a0-562e-86ad-a0b5c0de66d3]
Monitored metric elbo_validation did not improve in the last 45 records. Best score: -2342.332. Signaling Trainer to stop.
save model...
inferring perturbation...
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:18:16,316 - INFO - Using pre-computed Schur decomposition
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:18:27,849 - INFO - Using pre-computed Schur decomposition
Done alx4a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:18:38,951 - INFO - Using pre-computed Schur decomposition
Done arntl1b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:18:50,238 - INFO - Using pre-computed Schur decomposition
Done bach2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:19:01,405 - INFO - Using pre-computed Schur decomposition
Done bhlhe40
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:19:12,580 - INFO - Using pre-computed Schur decomposition
Done bhlhe41
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:19:23,358 - INFO - Using pre-computed Schur decomposition
Done dlx1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:19:34,878 - INFO - Using pre-computed Schur decomposition
Done ebf1b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:19:45,773 - INFO - Using pre-computed Schur decomposition
Done ebf3a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:19:56,866 - INFO - Using pre-computed Schur decomposition
Done egr1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:20:07,664 - INFO - Using pre-computed Schur decomposition
Done egr2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:20:18,700 - INFO - Using pre-computed Schur decomposition
Done egr3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:20:29,860 - INFO - Using pre-computed Schur decomposition
Done egr4
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:20:41,049 - INFO - Using pre-computed Schur decomposition
Done elf1
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:20:51,634 - INFO - Using pre-computed Schur decomposition
Done elk3
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:21:02,319 - INFO - Using pre-computed Schur decomposition
Done erf
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:21:13,590 - INFO - Using pre-computed Schur decomposition
Done erfl3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:21:24,357 - INFO - Using pre-computed Schur decomposition
Done ets1
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:21:35,276 - INFO - Using pre-computed Schur decomposition
Done etv5b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:21:46,352 - INFO - Using pre-computed Schur decomposition
Done fli1a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:21:57,121 - INFO - Using pre-computed Schur decomposition
Done fosab
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:22:08,099 - INFO - Using pre-computed Schur decomposition
Done fosl1a
INFO File
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el.pt already downloaded
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2024-11-24 13:22:18,737 - INFO - Using pre-computed Schur decomposition
Done fosl2
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:22:29,728 - INFO - Using pre-computed Schur decomposition
Done her9
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:22:40,883 - INFO - Using pre-computed Schur decomposition
Done hnf1ba
INFO File
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el.pt already downloaded
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2024-11-24 13:22:52,013 - INFO - Using pre-computed Schur decomposition
Done hnf1bb
INFO File
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el.pt already downloaded
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2024-11-24 13:23:03,038 - INFO - Using pre-computed Schur decomposition
Done hoxa11b
INFO File
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el.pt already downloaded
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2024-11-24 13:23:14,503 - INFO - Using pre-computed Schur decomposition
Done hoxa2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:23:25,385 - INFO - Using pre-computed Schur decomposition
Done hoxa4a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:23:36,200 - INFO - Using pre-computed Schur decomposition
Done hoxa9a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:23:47,137 - INFO - Using pre-computed Schur decomposition
Done hoxa9b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:23:57,937 - INFO - Using pre-computed Schur decomposition
Done hoxb10a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:24:08,798 - INFO - Using pre-computed Schur decomposition
Done hoxb1b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:24:20,112 - INFO - Using pre-computed Schur decomposition
Done hoxb5b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:24:31,273 - INFO - Using pre-computed Schur decomposition
Done hoxb9a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:24:41,977 - INFO - Using pre-computed Schur decomposition
Done hoxc11b
INFO File
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el.pt already downloaded
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2024-11-24 13:24:53,172 - INFO - Using pre-computed Schur decomposition
Done hoxc3a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:25:04,009 - INFO - Using pre-computed Schur decomposition
Done hoxc9a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:25:14,844 - INFO - Using pre-computed Schur decomposition
Done hoxd11a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:25:26,100 - INFO - Using pre-computed Schur decomposition
Done hoxd12a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:25:37,199 - INFO - Using pre-computed Schur decomposition
Done jdp2b
INFO File
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el.pt already downloaded
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2024-11-24 13:25:48,214 - INFO - Using pre-computed Schur decomposition
Done jun
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:25:59,034 - INFO - Using pre-computed Schur decomposition
Done junba
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:26:09,983 - INFO - Using pre-computed Schur decomposition
Done mitfa
INFO File
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el.pt already downloaded
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2024-11-24 13:26:22,529 - INFO - Using pre-computed Schur decomposition
Done msx1b
INFO File
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el.pt already downloaded
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2024-11-24 13:26:33,757 - INFO - Using pre-computed Schur decomposition
Done msx3
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:26:45,196 - INFO - Using pre-computed Schur decomposition
Done mycb
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:26:56,559 - INFO - Using pre-computed Schur decomposition
Done nfe2l2a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:27:07,802 - INFO - Using pre-computed Schur decomposition
Done nr2f2
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:27:19,172 - INFO - Using pre-computed Schur decomposition
Done nr2f5
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:27:30,605 - INFO - Using pre-computed Schur decomposition
Done nr2f6b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:27:41,925 - INFO - Using pre-computed Schur decomposition
Done nr4a2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:27:52,807 - INFO - Using pre-computed Schur decomposition
Done nr4a3
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:28:04,428 - INFO - Using pre-computed Schur decomposition
Done otx2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:28:16,487 - INFO - Using pre-computed Schur decomposition
Done pbx1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:28:27,556 - INFO - Using pre-computed Schur decomposition
Done pknox2
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:28:38,970 - INFO - Using pre-computed Schur decomposition
Done rarga
INFO File
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el.pt already downloaded
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WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:28:49,938 - INFO - Using pre-computed Schur decomposition
Done rxraa
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:29:00,947 - INFO - Using pre-computed Schur decomposition
Done snai1a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:29:12,053 - INFO - Using pre-computed Schur decomposition
Done sox10
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:29:23,029 - INFO - Using pre-computed Schur decomposition
Done sox6
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:29:34,225 - INFO - Using pre-computed Schur decomposition
Done sox9b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:29:45,619 - INFO - Using pre-computed Schur decomposition
Done tead1a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:29:56,534 - INFO - Using pre-computed Schur decomposition
Done tead1b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:30:07,459 - INFO - Using pre-computed Schur decomposition
Done tead3a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:30:18,461 - INFO - Using pre-computed Schur decomposition
Done tead3b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:30:29,987 - INFO - Using pre-computed Schur decomposition
Done tfap2a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_1/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:30:41,147 - INFO - Using pre-computed Schur decomposition
Done tfap2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:30:52,104 - INFO - Using pre-computed Schur decomposition
Done tfap2e
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:31:03,146 - INFO - Using pre-computed Schur decomposition
Done tfeb
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:31:14,104 - INFO - Using pre-computed Schur decomposition
Done tfec
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:31:24,988 - INFO - Using pre-computed Schur decomposition
Done twist1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:31:35,631 - INFO - Using pre-computed Schur decomposition
Done twist1b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:31:46,996 - INFO - Using pre-computed Schur decomposition
Done zeb1b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:31:58,252 - INFO - Using pre-computed Schur decomposition
Done zic2a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:32:09,497 - INFO - Using pre-computed Schur decomposition
Done zic2b
training model...
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [MIG-7294bf77-f0a0-562e-86ad-a0b5c0de66d3]
Monitored metric elbo_validation did not improve in the last 45 records. Best score: -2345.803. Signaling Trainer to stop.
save model...
inferring perturbation...
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:41:22,479 - INFO - Using pre-computed Schur decomposition
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:41:34,224 - INFO - Using pre-computed Schur decomposition
Done alx4a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:41:45,745 - INFO - Using pre-computed Schur decomposition
Done arntl1b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:41:57,104 - INFO - Using pre-computed Schur decomposition
Done bach2b
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el.pt already downloaded
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2024-11-24 13:42:08,342 - INFO - Using pre-computed Schur decomposition
Done bhlhe40
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el.pt already downloaded
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2024-11-24 13:42:19,519 - INFO - Using pre-computed Schur decomposition
Done bhlhe41
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:42:31,198 - INFO - Using pre-computed Schur decomposition
Done dlx1a
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:42:42,810 - INFO - Using pre-computed Schur decomposition
Done ebf1b
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:42:53,984 - INFO - Using pre-computed Schur decomposition
Done ebf3a
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:43:04,999 - INFO - Using pre-computed Schur decomposition
Done egr1
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:43:16,456 - INFO - Using pre-computed Schur decomposition
Done egr2b
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:43:27,679 - INFO - Using pre-computed Schur decomposition
Done egr3
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:43:38,679 - INFO - Using pre-computed Schur decomposition
Done egr4
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:43:49,871 - INFO - Using pre-computed Schur decomposition
Done elf1
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:44:01,187 - INFO - Using pre-computed Schur decomposition
Done elk3
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:44:13,022 - INFO - Using pre-computed Schur decomposition
Done erf
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:44:24,425 - INFO - Using pre-computed Schur decomposition
Done erfl3
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:44:35,709 - INFO - Using pre-computed Schur decomposition
Done ets1
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:44:46,812 - INFO - Using pre-computed Schur decomposition
Done etv5b
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:44:57,975 - INFO - Using pre-computed Schur decomposition
Done fli1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:45:09,080 - INFO - Using pre-computed Schur decomposition
Done fosab
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:45:20,533 - INFO - Using pre-computed Schur decomposition
Done fosl1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:45:32,637 - INFO - Using pre-computed Schur decomposition
Done fosl2
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:45:43,898 - INFO - Using pre-computed Schur decomposition
Done her9
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:45:55,347 - INFO - Using pre-computed Schur decomposition
Done hnf1ba
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:46:06,830 - INFO - Using pre-computed Schur decomposition
Done hnf1bb
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:46:18,393 - INFO - Using pre-computed Schur decomposition
Done hoxa11b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:46:30,213 - INFO - Using pre-computed Schur decomposition
Done hoxa2b
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:46:41,757 - INFO - Using pre-computed Schur decomposition
Done hoxa4a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:46:53,055 - INFO - Using pre-computed Schur decomposition
Done hoxa9a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:47:04,361 - INFO - Using pre-computed Schur decomposition
Done hoxa9b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:47:15,535 - INFO - Using pre-computed Schur decomposition
Done hoxb10a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:47:27,221 - INFO - Using pre-computed Schur decomposition
Done hoxb1b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:47:38,723 - INFO - Using pre-computed Schur decomposition
Done hoxb5b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:47:50,303 - INFO - Using pre-computed Schur decomposition
Done hoxb9a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:48:01,354 - INFO - Using pre-computed Schur decomposition
Done hoxc11b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:48:12,846 - INFO - Using pre-computed Schur decomposition
Done hoxc3a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:48:24,264 - INFO - Using pre-computed Schur decomposition
Done hoxc9a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:48:35,579 - INFO - Using pre-computed Schur decomposition
Done hoxd11a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:48:46,560 - INFO - Using pre-computed Schur decomposition
Done hoxd12a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:48:57,734 - INFO - Using pre-computed Schur decomposition
Done jdp2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:49:09,025 - INFO - Using pre-computed Schur decomposition
Done jun
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
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2024-11-24 13:49:20,355 - INFO - Using pre-computed Schur decomposition
Done junba
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:49:31,674 - INFO - Using pre-computed Schur decomposition
Done mitfa
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:49:43,296 - INFO - Using pre-computed Schur decomposition
Done msx1b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:49:54,826 - INFO - Using pre-computed Schur decomposition
Done msx3
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:50:06,358 - INFO - Using pre-computed Schur decomposition
Done mycb
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:50:17,888 - INFO - Using pre-computed Schur decomposition
Done nfe2l2a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:50:29,492 - INFO - Using pre-computed Schur decomposition
Done nr2f2
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:50:41,126 - INFO - Using pre-computed Schur decomposition
Done nr2f5
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:50:52,229 - INFO - Using pre-computed Schur decomposition
Done nr2f6b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:51:03,728 - INFO - Using pre-computed Schur decomposition
Done nr4a2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:51:14,804 - INFO - Using pre-computed Schur decomposition
Done nr4a3
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:51:26,917 - INFO - Using pre-computed Schur decomposition
Done otx2b
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:51:39,394 - INFO - Using pre-computed Schur decomposition
Done pbx1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:51:50,886 - INFO - Using pre-computed Schur decomposition
Done pknox2
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:52:02,783 - INFO - Using pre-computed Schur decomposition
Done rarga
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:52:14,269 - INFO - Using pre-computed Schur decomposition
Done rxraa
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:52:26,299 - INFO - Using pre-computed Schur decomposition
Done snai1a
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:52:38,199 - INFO - Using pre-computed Schur decomposition
Done sox10
INFO File
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el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:52:50,118 - INFO - Using pre-computed Schur decomposition
Done sox6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:53:02,438 - INFO - Using pre-computed Schur decomposition
Done sox9b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:53:14,664 - INFO - Using pre-computed Schur decomposition
Done tead1a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:53:26,393 - INFO - Using pre-computed Schur decomposition
Done tead1b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:53:37,678 - INFO - Using pre-computed Schur decomposition
Done tead3a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:53:49,429 - INFO - Using pre-computed Schur decomposition
Done tead3b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:54:01,311 - INFO - Using pre-computed Schur decomposition
Done tfap2a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:54:12,812 - INFO - Using pre-computed Schur decomposition
Done tfap2b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:54:24,545 - INFO - Using pre-computed Schur decomposition
Done tfap2e
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:54:36,508 - INFO - Using pre-computed Schur decomposition
Done tfeb
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:54:48,148 - INFO - Using pre-computed Schur decomposition
Done tfec
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:55:00,279 - INFO - Using pre-computed Schur decomposition
Done twist1a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:55:11,454 - INFO - Using pre-computed Schur decomposition
Done twist1b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:55:23,369 - INFO - Using pre-computed Schur decomposition
Done zeb1b
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:55:34,892 - INFO - Using pre-computed Schur decomposition
Done zic2a
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/zebrafish/processed/perturb_repeat_runs/rgv_model_2/mod
el.pt already downloaded
WARNING: Unable to import `petsc4py` or `slepc4py`. Using `method='brandts'`
WARNING: For `method='brandts'`, dense matrix is required. Densifying
2024-11-24 13:55:46,931 - INFO - Using pre-computed Schur decomposition
Done zic2b