Perturbation prediction on pancreatic endocrine via RegVelo#
Using RegVelo to perform perturbation prediction, under soft_mode each run will repeat run 15 models and aggregate prediction results
Library imports#
import numpy as np
import pandas as pd
import torch
import scanpy as sc
import scvi
from rgv_tools import DATA_DIR
from rgv_tools.perturbation import get_list_name, TFScanning
/home/icb/weixu.wang/miniconda3/envs/regvelo_test/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/regvelo_test/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/regvelo_test/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/regvelo_test/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/regvelo_test/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/regvelo_test/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/regvelo_test/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)
Matplotlib is building the font cache; this may take a moment.
General settings#
scvi.settings.seed = 0
[rank: 0] Seed set to 0
Constants#
DATASET = "pancreatic_endocrinogenesis"
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)
TERMINAL_STATES = ["Alpha", "Beta", "Delta", "Epsilon"]
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(0, 15):
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
print("inferring perturbation...")
perturb_screening = TFScanning(model, adata, 7, "clusters", TERMINAL_STATES, TF, 0, method="t-statistics")
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)
2024-11-27 01:50:50,675 - INFO - Using pre-computed Schur decomposition
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
WARNING: Using `7` components would split a block of complex conjugate eigenvalues. Using `n_components=8`
WARNING: Unable to compute macrostates with `n_states=7` because it will split complex conjugate eigenvalues. Using `n_states=8`
2024-11-27 01:51:29,595 - INFO - Using pre-computed Schur decomposition
Done Fhl2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 01:52:08,546 - INFO - Using pre-computed Schur decomposition
Done Klf7
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 01:52:47,153 - INFO - Using pre-computed Schur decomposition
Done Fev
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 01:53:25,613 - INFO - Using pre-computed Schur decomposition
Done Hes6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 01:54:04,379 - INFO - Using pre-computed Schur decomposition
Done Atf3
INFO File
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model_0/model.pt already downloaded
2024-11-27 01:54:42,535 - INFO - Using pre-computed Schur decomposition
Done Nuak2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 01:55:20,794 - INFO - Using pre-computed Schur decomposition
Done Tagln2
INFO File
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model_0/model.pt already downloaded
2024-11-27 01:55:58,812 - INFO - Using pre-computed Schur decomposition
Done Arg1
INFO File
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model_0/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 01:56:37,353 - INFO - Using pre-computed Schur decomposition
Done Foxo3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
2024-11-27 01:57:15,628 - INFO - Using pre-computed Schur decomposition
Done Hmga2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 01:57:53,975 - INFO - Using pre-computed Schur decomposition
Done Ikzf4
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
2024-11-27 01:58:32,221 - INFO - Using pre-computed Schur decomposition
Done Sim1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 01:59:10,392 - INFO - Using pre-computed Schur decomposition
Done Rfx6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
[0]PETSC ERROR:
2024-11-27 02:20:32,356 - INFO - Using pre-computed Schur decomposition
Done Nr4a2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
WARNING: Using `7` components would split a block of complex conjugate eigenvalues. Using `n_components=8`
[0]PETSC ERROR:
WARNING: Unable to compute macrostates with `n_states=7` because it will split complex conjugate eigenvalues. Using `n_states=8`
2024-11-27 02:21:11,956 - INFO - Using pre-computed Schur decomposition
Done Neurod1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
2024-11-27 02:21:52,095 - INFO - Using pre-computed Schur decomposition
Done Ehf
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 02:22:31,767 - INFO - Using pre-computed Schur decomposition
Done Cat
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2024-11-27 02:30:22,621 - INFO - Using pre-computed Schur decomposition
Done H2afz
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 02:31:01,926 - INFO - Using pre-computed Schur decomposition
Done Nfib
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 02:31:41,478 - INFO - Using pre-computed Schur decomposition
Done Prdm16
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/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 02:32:20,898 - INFO - Using pre-computed Schur decomposition
Done Mycl
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 02:32:59,644 - INFO - Using pre-computed Schur decomposition
Done Mnx1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 02:33:38,717 - INFO - Using pre-computed Schur decomposition
Done Nkx6-1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 02:34:18,366 - INFO - Using pre-computed Schur decomposition
Done Cdk2ap1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 02:34:57,627 - INFO - Using pre-computed Schur decomposition
Done Rest
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
2024-11-27 02:35:37,378 - INFO - Using pre-computed Schur decomposition
Done Msi1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_0/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
[0]PETSC ERROR: 2024-11-27 02:54:03,517 - INFO - Using pre-computed Schur decomposition
Done Foxo3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 02:54:43,089 - INFO - Using pre-computed Schur decomposition
Done Hmga2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 02:55:23,842 - INFO - Using pre-computed Schur decomposition
Done Ikzf4
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
2024-11-27 02:56:03,395 - INFO - Using pre-computed Schur decomposition
Done Sim1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR:
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2024-11-27 03:03:59,557 - INFO - Using pre-computed Schur decomposition
Done Irx1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 03:04:39,891 - INFO - Using pre-computed Schur decomposition
Done Isl1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
2024-11-27 03:05:18,820 - INFO - Using pre-computed Schur decomposition
Done Klf6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 03:05:58,383 - INFO - Using pre-computed Schur decomposition
Done Irx2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
2024-11-27 03:06:37,723 - INFO - Using pre-computed Schur decomposition
Done Zfhx2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: 2024-11-27 03:07:16,758 - INFO - Using pre-computed Schur decomposition
Done Dach1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 03:07:56,866 - INFO - Using pre-computed Schur decomposition
Done Vdr
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 03:08:35,687 - INFO - Using pre-computed Schur decomposition
Done Gpd1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 03:09:15,188 - INFO - Using pre-computed Schur decomposition
Done Nr4a1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR: ------------------------------------------------------------------------
2024-11-27 03:09:54,185 - INFO - Using pre-computed Schur decomposition
Done Etv5
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
[0]PETSC ERROR: 2024-11-27 03:30:48,047 - INFO - Using pre-computed Schur decomposition
Done Mnx1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
2024-11-27 03:31:26,982 - INFO - Using pre-computed Schur decomposition
Done Nkx6-1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 03:32:06,439 - INFO - Using pre-computed Schur decomposition
Done Cdk2ap1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
2024-11-27 03:32:45,271 - INFO - Using pre-computed Schur decomposition
Done Rest
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR:
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 03:41:07,027 - INFO - Using pre-computed Schur decomposition
Done Tead2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 03:41:45,627 - INFO - Using pre-computed Schur decomposition
Done Nfix
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
2024-11-27 03:42:24,184 - INFO - Using pre-computed Schur decomposition
Done Hmgb2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
2024-11-27 03:43:02,593 - INFO - Using pre-computed Schur decomposition
Done Hdac6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 03:43:40,982 - INFO - Using pre-computed Schur decomposition
Done Smarca1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
2024-11-27 03:44:19,345 - INFO - Using pre-computed Schur decomposition
Done Hmgb3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_1/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 03:44:58,462 - INFO - Using pre-computed Schur decomposition
Done Arx
inferring perturbation...
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 03:45:37,368 - INFO - Using pre-computed Schur decomposition
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 03:46:15,633 - INFO - Using pre-computed Schur decomposition
Done Fhl2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 03:46:54,019 - INFO - Using pre-computed Schur decomposition
Done Klf7
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2024-11-27 04:05:53,520 - INFO - Using pre-computed Schur decomposition
Done Gpd1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 04:06:32,864 - INFO - Using pre-computed Schur decomposition
Done Nr4a1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR:
2024-11-27 04:07:12,293 - INFO - Using pre-computed Schur decomposition
Done Etv5
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR:
2024-11-27 04:07:52,490 - INFO - Using pre-computed Schur decomposition
Done Zfp174
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR:
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
[0]PETSC ERROR: 2024-11-27 04:15:51,442 - INFO - Using pre-computed Schur decomposition
Done Nr4a2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 04:16:31,684 - INFO - Using pre-computed Schur decomposition
Done Neurod1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR:
2024-11-27 04:17:11,896 - INFO - Using pre-computed Schur decomposition
Done Ehf
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
2024-11-27 04:17:51,795 - INFO - Using pre-computed Schur decomposition
Done Cat
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
2024-11-27 04:18:31,359 - INFO - Using pre-computed Schur decomposition
Done Meis2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
2024-11-27 04:19:10,402 - INFO - Using pre-computed Schur decomposition
Done Nkx2-2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 04:19:49,605 - INFO - Using pre-computed Schur decomposition
Done Foxa2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR:
2024-11-27 04:20:29,389 - INFO - Using pre-computed Schur decomposition
Done E2f1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 04:21:08,315 - INFO - Using pre-computed Schur decomposition
Done Npdc1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_2/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
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To change this limit, set the config variable
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Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
2024-11-27 04:42:44,532 - INFO - Using pre-computed Schur decomposition
Done Arx
inferring perturbation...
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
2024-11-27 04:43:23,789 - INFO - Using pre-computed Schur decomposition
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
2024-11-27 04:44:02,685 - INFO - Using pre-computed Schur decomposition
Done Fhl2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
2024-11-27 04:44:41,852 - INFO - Using pre-computed Schur decomposition
Done Klf7
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
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To change this limit, set the config variable
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Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
[0]PETSC ERROR: 2024-11-27 04:51:51,170 - INFO - Using pre-computed Schur decomposition
Done Rfx6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 04:52:30,613 - INFO - Using pre-computed Schur decomposition
Done Hsf2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
2024-11-27 04:53:09,405 - INFO - Using pre-computed Schur decomposition
Done Neurog3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
2024-11-27 04:53:48,955 - INFO - Using pre-computed Schur decomposition
Done Neurod2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 04:54:27,969 - INFO - Using pre-computed Schur decomposition
Done Stat3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 04:55:07,619 - INFO - Using pre-computed Schur decomposition
Done Ebf1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 04:55:47,092 - INFO - Using pre-computed Schur decomposition
Done Sox9
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 04:56:26,117 - INFO - Using pre-computed Schur decomposition
Done Id2
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 04:57:05,526 - INFO - Using pre-computed Schur decomposition
Done Etv1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 04:57:45,051 - INFO - Using pre-computed Schur decomposition
Done Fos
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
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Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
Abort(59) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[0]PETSC ERROR: 2024-11-27 05:18:14,454 - INFO - Using pre-computed Schur decomposition
Done E2f1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 05:18:54,435 - INFO - Using pre-computed Schur decomposition
Done Npdc1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 05:19:34,051 - INFO - Using pre-computed Schur decomposition
Done Hspa5
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 05:20:14,325 - INFO - Using pre-computed Schur decomposition
Done Pax6
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_msg_rate_limit`.
Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)
Done Prdm16
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: 2024-11-27 05:25:32,025 - INFO - Using pre-computed Schur decomposition
Done Mycl
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 13 Broken Pipe: Likely while reading or writing to a socket
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
2024-11-27 05:26:11,500 - INFO - Using pre-computed Schur decomposition
Done Mnx1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: 2024-11-27 05:26:51,144 - INFO - Using pre-computed Schur decomposition
Done Nkx6-1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: ------------------------------------------------------------------------
2024-11-27 05:27:30,564 - INFO - Using pre-computed Schur decomposition
Done Cdk2ap1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 05:28:09,440 - INFO - Using pre-computed Schur decomposition
Done Rest
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 05:28:48,413 - INFO - Using pre-computed Schur decomposition
Done Msi1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR:
[0]PETSC ERROR: 2024-11-27 05:29:27,457 - INFO - Using pre-computed Schur decomposition
Done Mlxipl
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
[0]PETSC ERROR: 2024-11-27 05:30:06,995 - INFO - Using pre-computed Schur decomposition
Done Srrm3
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
2024-11-27 05:30:46,482 - INFO - Using pre-computed Schur decomposition
Done Pdx1
INFO File
/ictstr01/home/icb/weixu.wang/regulatory_velo/data/pancreatic_endocrine/processed/perturb_repeat_runs/rgv_
model_3/model.pt already downloaded
IOPub message rate exceeded.
The Jupyter server will temporarily stop sending output
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To change this limit, set the config variable
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Current values:
ServerApp.iopub_msg_rate_limit=1000.0 (msgs/sec)
ServerApp.rate_limit_window=3.0 (secs)