Run TFvelo on mHSPC datasets

Library import

from itertools import permutations, product

import TFvelo as TFv

import numpy as np
import pandas as pd
import scipy
from sklearn.metrics import roc_auc_score

import scanpy as sc

from rgv_tools import DATA_DIR

/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: FutureWarning: Importing CSCDataset from `anndata.experimental` is deprecated. Import anndata.abc.CSCDataset instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: FutureWarning: Importing CSRDataset from `anndata.experimental` is deprecated. Import anndata.abc.CSRDataset instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: FutureWarning: Importing read_elem from `anndata.experimental` is deprecated. Import anndata.io.read_elem instead.
  warnings.warn(msg, FutureWarning)
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/jaxlib/plugin_support.py:71: RuntimeWarning: JAX plugin jax_cuda12_plugin version 0.5.0 is installed, but it is not compatible with the installed jaxlib version 0.6.2, so it will not be used.
  warnings.warn(

Constants

DATASET = "mHSPC"

SAVE_DATA = True
if SAVE_DATA:
    (DATA_DIR / DATASET / "results").mkdir(parents=True, exist_ok=True)

Define functions

We followed the GRN benchmark workflow provided by BEELINE, please check Murali-group/Beeline

def unsigned(true_edges: pd.DataFrame, pred_edges: pd.DataFrame, type: str = "alledges") -> tuple[float, float, float]:
    """Compare true vs predicted edges (unsigned) and compute precision/recall metrics.

    Returns
    -------
        tuple: (eprec, erec, eprec_ratio)
    """
    true_edges_copy = true_edges.copy()
    pred_edges_copy = pred_edges.copy()

    # Drop self-edges and duplicates
    true_edges_copy = true_edges_copy.loc[(true_edges_copy["Gene1"] != true_edges_copy["Gene2"])]
    true_edges_copy.drop_duplicates(keep="first", inplace=True)
    true_edges_copy.reset_index(drop=True, inplace=True)

    pred_edges_copy = pred_edges_copy.loc[(pred_edges_copy["Gene1"] != pred_edges_copy["Gene2"])]
    pred_edges_copy.drop_duplicates(keep="first", inplace=True)
    pred_edges_copy.reset_index(drop=True, inplace=True)

    # Get a list of all possible TF to gene interactions
    unique_nodes = np.unique(true_edges_copy.loc[:, ["Gene1", "Gene2"]])
    possible_edges_all = set(product(set(true_edges_copy.Gene1), set(unique_nodes)))

    # Get a list of all possible interactions
    possible_edges_no_self = set(permutations(unique_nodes, r=2))

    # Find intersection of above lists to ignore self edges
    possible_edges = possible_edges_all.intersection(possible_edges_no_self)

    true_edges_dict = {"|".join(p): 0 for p in possible_edges}

    true_edges_str = true_edges_copy["Gene1"] + "|" + true_edges_copy["Gene2"]
    true_edges_str = true_edges_str[true_edges_str.isin(true_edges_dict)]
    n_edges = len(true_edges_str)

    pred_edges_copy["Edges"] = pred_edges_copy["Gene1"] + "|" + pred_edges_copy["Gene2"]
    pred_edges_copy = pred_edges_copy[pred_edges_copy["Edges"].isin(true_edges_dict)]
    pred_edges_copy.copy()

    if not pred_edges_copy.shape[0] == 0:
        pred_edges_copy.loc[:, "EdgeWeight"] = pred_edges_copy.EdgeWeight.round(6).abs()
        pred_edges_copy.sort_values(by="EdgeWeight", ascending=False, inplace=True)

        maxk = min(pred_edges_copy.shape[0], n_edges)
        edge_weight_topk = pred_edges_copy.iloc[maxk - 1].EdgeWeight

        nnz_min = np.nanmin(pred_edges_copy.EdgeWeight.replace(0, np.nan).values)
        best_val = max(nnz_min, edge_weight_topk)

        newDF = pred_edges_copy.loc[(pred_edges_copy["EdgeWeight"] >= best_val)]
        rank = set(newDF["Gene1"] + "|" + newDF["Gene2"])

        intersectionSet = rank.intersection(true_edges_str)
        eprec = len(intersectionSet) / len(rank)
        erec = len(intersectionSet) / len(true_edges_str)

        random_eprec = n_edges / len(true_edges_dict)
        eprec_ratio = eprec / random_eprec
    else:
        eprec = 1.0
        erec = 1.0
        eprec_ratio = 1.0

    print("EPR: " + str(eprec_ratio))
    return eprec, erec, eprec_ratio


def calculate_auroc(inferred_scores_df: pd.DataFrame, ground_truth_df: pd.DataFrame) -> float:
    """Calculate AUROC comparing inferred edge scores against ground truth.

    Returns
    -------
        float: AUROC score.
    """
    ground_truth_set = set(zip(ground_truth_df["Gene1"], ground_truth_df["Gene2"]))

    inferred_scores_df["label"] = inferred_scores_df.apply(
        lambda row: (row["Gene1"], row["Gene2"]) in ground_truth_set, axis=1
    ).astype(int)

    y_true = inferred_scores_df["label"]
    y_scores = inferred_scores_df["EdgeWeight"]

    auroc = roc_auc_score(y_true, y_scores)
    return auroc

def run_TFvelo(adata, TF):
    """TFvelo pipeline."""
    adata.X = adata.X.toarray()
    n_gene = adata.shape[1]
    adata.varm["TFs"] = np.full([n_gene, n_gene], "blank")
    adata.varm["TFs"] = adata.varm["TFs"].astype("U10")

    adata.varm["TFs_id"] = np.full([n_gene, n_gene], -1)
    adata.varm["TFs_times"] = np.full([n_gene, n_gene], 0)
    adata.varm["TFs_correlation"] = np.full([n_gene, n_gene], 0.0)
    adata.varm["knockTF_Log2FC"] = np.full([n_gene, n_gene], 0.0)
    adata.var["n_TFs"] = np.zeros(n_gene, dtype=int)

    gene_names = adata.var_names.tolist()  # all genes as targets
    all_TFs = list(TF)  # select TFs

    for TF_name in all_TFs:
        TF_idx = gene_names.index(TF_name)
        TF_expression = np.ravel(adata[:, TF_name].X)

        for target in gene_names:
            target_idx = gene_names.index(target)
            if target == TF_name:
                continue

            if TF_name in adata.varm["TFs"][target_idx]:
                ii = list(adata.varm["TFs"][target_idx]).index(TF_name)
                adata.varm["TFs_times"][target_idx, ii] += 1
                continue
            target_expression = np.ravel(adata[:, target].X)
            flag = (TF_expression > 0) & (target_expression > 0)  # consider all possible regulation
            if flag.sum() < 2:
                correlation = 0
            else:
                correlation, _ = scipy.stats.spearmanr(target_expression[flag], TF_expression[flag])

            tmp_n_TF = adata.var["n_TFs"][target_idx]
            adata.varm["TFs"][target_idx][tmp_n_TF] = TF_name
            adata.varm["TFs_id"][target_idx][tmp_n_TF] = TF_idx
            adata.varm["TFs_times"][target_idx, tmp_n_TF] = 1
            adata.varm["TFs_correlation"][target_idx, tmp_n_TF] = correlation
            adata.var["n_TFs"][target_idx] += 1

    TFv.tl.recover_dynamics(
        adata,
        n_jobs=64,
        max_iter=20,
        var_names="all",
        WX_method="lsq_linear",
        WX_thres=20,
        n_top_genes=adata.shape[1],
        fit_scaling=True,
        use_raw=0,
        init_weight_method="ones",
        n_time_points=1000,
    )
    n_cells = adata.shape[0]
    expanded_scaling_y = np.expand_dims(np.array(adata.var["fit_scaling_y"]), 0).repeat(n_cells, axis=0)
    adata.layers["velocity"] = adata.layers["velo_hat"] / expanded_scaling_y
    return adata

Data loading

adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "mHSC_ExpressionData.h5ad")

TF = pd.read_csv(DATA_DIR / DATASET / "raw" / "mouse-tfs.csv")
TF = [i[0].upper() + i[1:].lower() for i in TF["TF"].tolist()]

TF = np.array(TF)[[i in adata.var_names for i in TF]]

TF

array(['Ankrd22', 'Ankrd7', 'Arntl2', 'Batf3', 'Bcl11b', 'Bmp6', 'Btg2',
       'Chd7', 'Ciita', 'Cnot6l', 'Creb5', 'Csrp3', 'Ctr9', 'Ebf1',
       'Egr2', 'Esr1', 'Ets1', 'Etv6', 'Eya1', 'Eya2', 'Eya4', 'Fos',
       'Fosb', 'Gata1', 'Gata2', 'Gata3', 'Gfi1', 'Gfi1b', 'Glis3', 'Hlf',
       'Hoxa9', 'Hspb1', 'Id2', 'Id3', 'Ifi204', 'Ikzf1', 'Ikzf3', 'Il10',
       'Irf4', 'Irf8', 'Isl1', 'Klf1', 'Klf6', 'Kpna2', 'Ldb2', 'Lef1',
       'Lmo4', 'Maf', 'Mapk11', 'Mecom', 'Mef2c', 'Meis1', 'Mllt3',
       'Mmp9', 'Myb', 'Myc', 'Mycn', 'Nfatc2', 'Nfia', 'Nfil3', 'Nfkbiz',
       'Nr1h4', 'Pax5', 'Pgr', 'Pou2af1', 'Prdm1', 'Rad54b', 'Rapgef3',
       'Relb', 'Rora', 'Runx1t1', 'Satb1', 'Setbp1', 'Sla2', 'Smarca4',
       'Spib', 'Stat3', 'Stat4', 'Tox2', 'Trib3', 'Trps1', 'Xbp1',
       'Zbtb16', 'Zbtb20', 'Zbtb38', 'Zfp354a'], dtype='<U12')

Velocity pipeline

adata.layers["total"] = adata.X
adata.layers["total_raw"] = adata.layers["total"].copy()

TFv.pp.moments(adata, n_pcs=None, n_neighbors=None)

adata = run_TFvelo(adata, TF)

computing moments based on connectivities
    finished (0:00:00) --> added 
    'M_total', moments of total abundances (adata.layers)
recovering dynamics (using 64/112 cores)

/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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-py310/lib/python3.10/site-packages/anndata/utils.py:434: 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/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound
/home/icb/weixu.wang/miniconda3/envs/regvelo-py310/lib/python3.10/site-packages/louvain/__init__.py:54: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import get_distribution, DistributionNotFound

WARNING: 0/17 Vmn1r35 not recoverable due to insufficient samples.
WARNING: 1/17 Igkv10-96 not recoverable due to insufficient samples.
WARNING: 2/17 Igkv4-92 not recoverable due to insufficient samples.
WARNING: 3/17 Igkv12-89 not recoverable due to insufficient samples.
WARNING: 4/17 Igkv4-50 not recoverable due to insufficient samples.
WARNING: 5/17 Igkv5-39 not recoverable due to insufficient samples.
Processing 6/17 Igkv8-34
6/17 Igkv8-34 FINISHED with n_TFs: 86
Processing 7/17 Exoc6b
7/17 Exoc6b FINISHED with n_TFs: 86
WARNING: 8/17 Gkn3 not recoverable due to insufficient samples.
Processing 9/17 Arhgap25
9/17 Arhgap25 FINISHED with n_TFs: 86
WARNING: 10/17 Il5ra not recoverable due to insufficient samples.
WARNING: 11/17 Alox5 not recoverable due to insufficient samples.
Processing 12/17 Rassf4
12/17 Rassf4 FINISHED with n_TFs: 86
Processing 13/17 Cd9
13/17 Cd9 FINISHED with n_TFs: 86
Processing 14/17 BC035044
14/17 BC035044 FINISHED with n_TFs: 86
Processing 15/17 Cd69
15/17 Cd69 FINISHED with n_TFs: 86
WARNING: 16/17 Clec12b not recoverable due to insufficient samples.
Processing 0/17 Sel1l
0/17 Sel1l FINISHED with n_TFs: 86
WARNING: 1/17 Tc2n not recoverable due to insufficient samples.
WARNING: 2/17 Bcl11b not recoverable due to insufficient samples.
WARNING: 3/17 Ahnak2 not recoverable due to insufficient samples.
WARNING: 4/17 Ighg3 not recoverable due to insufficient samples.
Processing 5/17 Ighd
5/17 Ighd FINISHED with n_TFs: 86
Processing 6/17 Ighm
6/17 Ighm FINISHED with n_TFs: 86
WARNING: 7/17 Ighv2-2 not recoverable due to insufficient samples.
WARNING: 8/17 Ighv9-1 not recoverable due to insufficient samples.
WARNING: 9/17 Ighv9-3 not recoverable due to insufficient samples.
Processing 10/17 Ighv6-3
10/17 Ighv6-3 FINISHED with n_TFs: 86
Processing 11/17 Ighv6-6
11/17 Ighv6-6 FINISHED with n_TFs: 86
WARNING: 12/17 Ighv10-1 not recoverable due to insufficient samples.
Processing 13/17 Ighv1-9
13/17 Ighv1-9 FINISHED with n_TFs: 86
Processing 14/17 Ighv1-58
14/17 Ighv1-58 FINISHED with n_TFs: 86
WARNING: 15/17 Ighv8-12 not recoverable due to insufficient samples.
Processing 16/17 Ighv1-81
16/17 Ighv1-81 FINISHED with n_TFs: 86
WARNING: 0/17 Id3 not recoverable due to insufficient samples.
Processing 1/17 Dhrs3
1/17 Dhrs3 FINISHED with n_TFs: 86
Processing 2/17 Tnfrsf25
2/17 Tnfrsf25 FINISHED with n_TFs: 86
WARNING: 3/17 Ttc34 not recoverable due to insufficient samples.
Processing 4/17 C1qtnf12
4/17 C1qtnf12 FINISHED with n_TFs: 86
Processing 5/17 Cdk14
5/17 Cdk14 FINISHED with n_TFs: 86
Processing 6/17 Adam22
6/17 Adam22 FINISHED with n_TFs: 86
WARNING: 7/17 4921504A21Rik not recoverable due to insufficient samples.
Processing 8/17 Fbxl13
8/17 Fbxl13 FINISHED with n_TFs: 86
WARNING: 9/17 Reln not recoverable due to insufficient samples.
WARNING: 10/17 Zfyve28 not recoverable due to insufficient samples.
Processing 11/17 Sorcs2
11/17 Sorcs2 FINISHED with n_TFs: 86
WARNING: 12/17 Evc not recoverable due to insufficient samples.
Processing 13/17 Hs3st1
13/17 Hs3st1 FINISHED with n_TFs: 86
WARNING: 14/17 Prom1 not recoverable due to insufficient samples.
WARNING: 15/17 Ldb2 not recoverable due to insufficient samples.
WARNING: 16/17 Tlr1 not recoverable due to insufficient samples.
WARNING: 0/17 Olr1 not recoverable due to insufficient samples.
WARNING: 1/17 Klrk1 not recoverable due to insufficient samples.
WARNING: 2/17 Klrc1 not recoverable due to insufficient samples.
WARNING: 3/17 Klra4 not recoverable due to insufficient samples.
WARNING: 4/17 Klra7 not recoverable due to insufficient samples.
Processing 5/17 Plbd1
5/17 Plbd1 FINISHED with n_TFs: 86
Processing 6/17 Eps8
6/17 Eps8 FINISHED with n_TFs: 86
Processing 7/17 Gm6288
7/17 Gm6288 FINISHED with n_TFs: 86
Processing 8/17 Gm17216
8/17 Gm17216 FINISHED with n_TFs: 86
Processing 9/17 Ppp1r9a
9/17 Ppp1r9a FINISHED with n_TFs: 86
WARNING: 10/17 Ankrd7 not recoverable due to insufficient samples.
WARNING: 11/17 Ccdc136 not recoverable due to insufficient samples.
Processing 12/17 Tbxas1
12/17 Tbxas1 FINISHED with n_TFs: 86
Processing 13/17 Rab19
13/17 Rab19 FINISHED with n_TFs: 86
WARNING: 14/17 Trbc1 not recoverable due to insufficient samples.
Processing 15/17 Trbc2
15/17 Trbc2 FINISHED with n_TFs: 86
WARNING: 16/17 Sspo not recoverable due to insufficient samples.
Processing 0/17 Emb
0/17 Emb FINISHED with n_TFs: 86
WARNING: 1/17 Gm3248 not recoverable due to insufficient samples.
WARNING: 2/17 Dnase1l3 not recoverable due to insufficient samples.
Processing 3/17 Gm21738
3/17 Gm21738 FINISHED with n_TFs: 86
WARNING: 4/17 Gm30363 not recoverable due to insufficient samples.
WARNING: 5/17 Dupd1 not recoverable due to insufficient samples.
Processing 6/17 Cacna1d
6/17 Cacna1d FINISHED with n_TFs: 86
WARNING: 7/17 Colq not recoverable due to insufficient samples.
WARNING: 8/17 Sh2d4b not recoverable due to insufficient samples.
Processing 9/17 Tspan14
9/17 Tspan14 FINISHED with n_TFs: 86
WARNING: 10/17 4930431P03Rik not recoverable due to insufficient samples.
WARNING: 11/17 Rnase12 not recoverable due to insufficient samples.
WARNING: 12/17 Gm29776 not recoverable due to insufficient samples.
Processing 13/17 Slc7a8
13/17 Slc7a8 FINISHED with n_TFs: 86
Processing 14/17 Mcpt8
14/17 Mcpt8 FINISHED with n_TFs: 86
Processing 15/17 Ctsg
15/17 Ctsg FINISHED with n_TFs: 86
Processing 16/17 Gzmb
16/17 Gzmb FINISHED with n_TFs: 86
WARNING: 0/17 Lifr not recoverable due to insufficient samples.
WARNING: 1/17 Prlr not recoverable due to insufficient samples.
WARNING: 2/17 Ctnnd2 not recoverable due to insufficient samples.
WARNING: 3/17 Gm32618 not recoverable due to insufficient samples.
Processing 4/17 Sdc2
4/17 Sdc2 FINISHED with n_TFs: 86
Processing 5/17 Spag1
5/17 Spag1 FINISHED with n_TFs: 86
WARNING: 6/17 Dcstamp not recoverable due to insufficient samples.
Processing 7/17 Myc
7/17 Myc FINISHED with n_TFs: 85
WARNING: 8/17 Gm2895 not recoverable due to insufficient samples.
Processing 9/17 Apol9b
9/17 Apol9b FINISHED with n_TFs: 86
Processing 10/17 Lgals1
10/17 Lgals1 FINISHED with n_TFs: 86
Processing 11/17 Creld2
11/17 Creld2 FINISHED with n_TFs: 86
WARNING: 12/17 Cntn1 not recoverable due to insufficient samples.
WARNING: 13/17 Acvrl1 not recoverable due to insufficient samples.
Processing 14/17 Tns2
14/17 Tns2 FINISHED with n_TFs: 86
WARNING: 15/17 Gm4544 not recoverable due to insufficient samples.
Processing 16/17 Igll1
16/17 Igll1 FINISHED with n_TFs: 86
WARNING: 0/17 Gm33858 not recoverable due to insufficient samples.
WARNING: 1/17 Ackr2 not recoverable due to insufficient samples.
WARNING: 2/17 Ccr2 not recoverable due to insufficient samples.
Processing 3/17 Gata1
3/17 Gata1 FINISHED with n_TFs: 85
WARNING: 4/17 Cybb not recoverable due to insufficient samples.
Processing 5/17 Cfp
5/17 Cfp FINISHED with n_TFs: 86
Processing 6/17 Zfp300
6/17 Zfp300 FINISHED with n_TFs: 86
WARNING: 7/17 Hs6st2 not recoverable due to insufficient samples.
Processing 8/17 Arhgef6
8/17 Arhgef6 FINISHED with n_TFs: 86
Processing 9/17 Fgf13
9/17 Fgf13 FINISHED with n_TFs: 86
Processing 10/17 Gabre
10/17 Gabre FINISHED with n_TFs: 86
WARNING: 11/17 Gm4779 not recoverable due to insufficient samples.
WARNING: 12/17 Nox1 not recoverable due to insufficient samples.
Processing 13/17 Tlr7
13/17 Tlr7 FINISHED with n_TFs: 86
Processing 14/17 Gm14379
14/17 Gm14379 FINISHED with n_TFs: 86
WARNING: 15/17 Cacna1f not recoverable due to insufficient samples.
Processing 16/17 Pim2
16/17 Pim2 FINISHED with n_TFs: 86
Processing 0/17 Gnb4
0/17 Gnb4 FINISHED with n_TFs: 86
Processing 1/17 Ccna2
1/17 Ccna2 FINISHED with n_TFs: 86
WARNING: 2/17 Rarres1 not recoverable due to insufficient samples.
Processing 3/17 Trim59
3/17 Trim59 FINISHED with n_TFs: 86
WARNING: 4/17 Gria2 not recoverable due to insufficient samples.
Processing 5/17 Tdo2
5/17 Tdo2 FINISHED with n_TFs: 86
Processing 6/17 Gucy1a1
6/17 Gucy1a1 FINISHED with n_TFs: 86
WARNING: 7/17 Rbm46 not recoverable due to insufficient samples.
Processing 8/17 Trim2
8/17 Trim2 FINISHED with n_TFs: 86
WARNING: 9/17 Fcrls not recoverable due to insufficient samples.
Processing 10/17 Pear1
10/17 Pear1 FINISHED with n_TFs: 86
WARNING: 11/17 Rhbg not recoverable due to insufficient samples.
Processing 12/17 Chrnb2
12/17 Chrnb2 FINISHED with n_TFs: 86
Processing 13/17 S100a9
13/17 S100a9 FINISHED with n_TFs: 86
WARNING: 14/17 Adamtsl4 not recoverable due to insufficient samples.
WARNING: 15/17 Gm20627 not recoverable due to insufficient samples.
WARNING: 16/17 Cd2 not recoverable due to insufficient samples.
WARNING: 0/17 Bace2 not recoverable due to insufficient samples.
Processing 1/17 Slc22a3
1/17 Slc22a3 FINISHED with n_TFs: 86
Processing 2/17 Pnldc1
2/17 Pnldc1 FINISHED with n_TFs: 86
WARNING: 3/17 Fpr1 not recoverable due to insufficient samples.
WARNING: 4/17 Prss30 not recoverable due to insufficient samples.
Processing 5/17 Ccnf
5/17 Ccnf FINISHED with n_TFs: 86
WARNING: 6/17 Cacna1h not recoverable due to insufficient samples.
Processing 7/17 Rasal3
7/17 Rasal3 FINISHED with n_TFs: 86
WARNING: 8/17 Zfp811 not recoverable due to insufficient samples.
Processing 9/17 H2-Aa
9/17 H2-Aa FINISHED with n_TFs: 86
WARNING: 10/17 Mpig6b not recoverable due to insufficient samples.
WARNING: 11/17 Lta not recoverable due to insufficient samples.
WARNING: 12/17 H2-M5 not recoverable due to insufficient samples.
Processing 13/17 Crisp2
13/17 Crisp2 FINISHED with n_TFs: 86
Processing 14/17 Daam2
14/17 Daam2 FINISHED with n_TFs: 86
Processing 15/17 Dazl
15/17 Dazl FINISHED with n_TFs: 86
Processing 16/17 Satb1
16/17 Satb1 FINISHED with n_TFs: 85
WARNING: 0/17 Spib not recoverable due to insufficient samples.
Processing 1/17 Csrp3
1/17 Csrp3 FINISHED with n_TFs: 85
WARNING: 2/17 Dgat2 not recoverable due to insufficient samples.
Processing 3/17 Hbb-bt
3/17 Hbb-bt FINISHED with n_TFs: 86
WARNING: 4/17 Hbb-bs not recoverable due to insufficient samples.
Processing 5/17 Trim30d
5/17 Trim30d FINISHED with n_TFs: 86
Processing 6/17 Sbf2
6/17 Sbf2 FINISHED with n_TFs: 86
Processing 7/17 Mrvi1
7/17 Mrvi1 FINISHED with n_TFs: 86
WARNING: 8/17 Zkscan2 not recoverable due to insufficient samples.
Processing 9/17 Cd19
9/17 Cd19 FINISHED with n_TFs: 86
Processing 10/17 Sult1a1
10/17 Sult1a1 FINISHED with n_TFs: 86
WARNING: 11/17 Prss8 not recoverable due to insufficient samples.
Processing 12/17 Chst15
12/17 Chst15 FINISHED with n_TFs: 86
Processing 13/17 Mki67
13/17 Mki67 FINISHED with n_TFs: 86
WARNING: 14/17 Tcerg1l not recoverable due to insufficient samples.
Processing 15/17 Adam8
15/17 Adam8 FINISHED with n_TFs: 86
WARNING: 16/17 Syce1 not recoverable due to insufficient samples.
Processing 0/17 Ifitm5
0/17 Ifitm5 FINISHED with n_TFs: 86
WARNING: 1/17 Trpm5 not recoverable due to insufficient samples.
WARNING: 2/17 Ncr1 not recoverable due to insufficient samples.
Processing 3/17 Rnf225
3/17 Rnf225 FINISHED with n_TFs: 86
WARNING: 4/17 Cd79a not recoverable due to insufficient samples.
Processing 5/17 Blvrb
5/17 Blvrb FINISHED with n_TFs: 86
Processing 6/17 Fbxo27
6/17 Fbxo27 FINISHED with n_TFs: 86
WARNING: 7/17 Rasgrp4 not recoverable due to insufficient samples.
Processing 8/17 Clip3
8/17 Clip3 FINISHED with n_TFs: 86
Processing 9/17 Tyrobp
9/17 Tyrobp FINISHED with n_TFs: 86
WARNING: 10/17 Gm10640 not recoverable due to insufficient samples.
Processing 11/17 Siglecf
11/17 Siglecf FINISHED with n_TFs: 86
Processing 12/17 Nkg7
12/17 Nkg7 FINISHED with n_TFs: 86
Processing 13/17 Vsig10l
13/17 Vsig10l FINISHED with n_TFs: 86
WARNING: 14/17 Fut1 not recoverable due to insufficient samples.
WARNING: 15/17 Siglech not recoverable due to insufficient samples.
Processing 16/17 Atp10a
16/17 Atp10a FINISHED with n_TFs: 86
WARNING: 0/18 Zap70 not recoverable due to insufficient samples.
Processing 1/18 Il1r2
1/18 Il1r2 FINISHED with n_TFs: 86
Processing 2/18 Il1r1
2/18 Il1r1 FINISHED with n_TFs: 86
Processing 3/18 Il18rap
3/18 Il18rap FINISHED with n_TFs: 86
Processing 4/18 Stat4
4/18 Stat4 FINISHED with n_TFs: 85
Processing 5/18 Plcl1
5/18 Plcl1 FINISHED with n_TFs: 86
WARNING: 6/18 Spats2l not recoverable due to insufficient samples.
WARNING: 7/18 Cd28 not recoverable due to insufficient samples.
Processing 8/18 Wnt6
8/18 Wnt6 FINISHED with n_TFs: 86
WARNING: 9/18 Wnt10a not recoverable due to insufficient samples.
Processing 10/18 Slc4a3
10/18 Slc4a3 FINISHED with n_TFs: 86
Processing 11/18 Rbm44
11/18 Rbm44 FINISHED with n_TFs: 86
WARNING: 12/18 Klhl30 not recoverable due to insufficient samples.
WARNING: 13/18 Il10 not recoverable due to insufficient samples.
Processing 14/18 Ctse
14/18 Ctse FINISHED with n_TFs: 86
WARNING: 15/18 Rab7b not recoverable due to insufficient samples.
Processing 16/18 Slc45a3
16/18 Slc45a3 FINISHED with n_TFs: 86
WARNING: 17/18 Etnk2 not recoverable due to insufficient samples.
Processing 0/17 Afap1
0/17 Afap1 FINISHED with n_TFs: 86
WARNING: 1/17 Evc2 not recoverable due to insufficient samples.
WARNING: 2/17 Bst1 not recoverable due to insufficient samples.
Processing 3/17 Cd38
3/17 Cd38 FINISHED with n_TFs: 86
WARNING: 4/17 Slit2 not recoverable due to insufficient samples.
WARNING: 5/17 Slc4a4 not recoverable due to insufficient samples.
Processing 6/17 Pf4
6/17 Pf4 FINISHED with n_TFs: 86
Processing 7/17 Parm1
7/17 Parm1 FINISHED with n_TFs: 86
Processing 8/17 Anxa3
8/17 Anxa3 FINISHED with n_TFs: 86
WARNING: 9/17 Ptpn13 not recoverable due to insufficient samples.
Processing 10/17 Spp1
10/17 Spp1 FINISHED with n_TFs: 86
WARNING: 11/17 A630023P12Rik not recoverable due to insufficient samples.
Processing 12/17 Mn1
12/17 Mn1 FINISHED with n_TFs: 86
Processing 13/17 Oasl2
13/17 Oasl2 FINISHED with n_TFs: 86
WARNING: 14/17 Rflna not recoverable due to insufficient samples.
Processing 15/17 Hspb1
15/17 Hspb1 FINISHED with n_TFs: 85
Processing 16/17 Rasa4
16/17 Rasa4 FINISHED with n_TFs: 86
Processing 0/17 H2-Q6
0/17 H2-Q6 FINISHED with n_TFs: 86
Processing 1/17 Rhag
1/17 Rhag FINISHED with n_TFs: 86
WARNING: 2/17 Trem3 not recoverable due to insufficient samples.
Processing 3/17 B430306N03Rik
3/17 B430306N03Rik FINISHED with n_TFs: 86
WARNING: 4/17 Treml1 not recoverable due to insufficient samples.
WARNING: 5/17 Gm19585 not recoverable due to insufficient samples.
Processing 6/17 Uhrf1
6/17 Uhrf1 FINISHED with n_TFs: 86
Processing 7/17 Epb41l3
7/17 Epb41l3 FINISHED with n_TFs: 86
Processing 8/17 Ltbp1
8/17 Ltbp1 FINISHED with n_TFs: 86
WARNING: 9/17 Rasgrp3 not recoverable due to insufficient samples.
Processing 10/17 1810073O08Rik
10/17 1810073O08Rik FINISHED with n_TFs: 86
WARNING: 11/17 Epcam not recoverable due to insufficient samples.
Processing 12/17 Zfp521
12/17 Zfp521 FINISHED with n_TFs: 86
WARNING: 13/17 Cdh2 not recoverable due to insufficient samples.
Processing 14/17 B4galt6
14/17 B4galt6 FINISHED with n_TFs: 86
WARNING: 15/17 Mzb1 not recoverable due to insufficient samples.
Processing 16/17 Fech
16/17 Fech FINISHED with n_TFs: 86
Processing 0/17 5033403F01Rik
0/17 5033403F01Rik FINISHED with n_TFs: 86
Processing 1/17 Tmem14c
1/17 Tmem14c FINISHED with n_TFs: 86
WARNING: 2/17 Gm10790 not recoverable due to insufficient samples.
WARNING: 3/17 Cd83 not recoverable due to insufficient samples.
WARNING: 4/17 Gm33195 not recoverable due to insufficient samples.
WARNING: 5/17 4921525O09Rik not recoverable due to insufficient samples.
Processing 6/17 Cplx2
6/17 Cplx2 FINISHED with n_TFs: 86
WARNING: 7/17 Slc34a1 not recoverable due to insufficient samples.
WARNING: 8/17 Slc6a3 not recoverable due to insufficient samples.
Processing 9/17 Clptm1l
9/17 Clptm1l FINISHED with n_TFs: 86
Processing 10/17 Tert
10/17 Tert FINISHED with n_TFs: 86
Processing 11/17 Mctp1
11/17 Mctp1 FINISHED with n_TFs: 86
Processing 12/17 Mef2c
12/17 Mef2c FINISHED with n_TFs: 85
Processing 13/17 Lhfpl2
13/17 Lhfpl2 FINISHED with n_TFs: 86
Processing 14/17 Plk2
14/17 Plk2 FINISHED with n_TFs: 86
WARNING: 15/17 Ankrd55 not recoverable due to insufficient samples.
Processing 16/17 Il6st
16/17 Il6st FINISHED with n_TFs: 86
Processing 0/18 Mpzl1
0/18 Mpzl1 FINISHED with n_TFs: 86
Processing 1/18 Rcsd1
1/18 Rcsd1 FINISHED with n_TFs: 86
WARNING: 2/18 Fcrla not recoverable due to insufficient samples.
Processing 3/18 Fcer1g
3/18 Fcer1g FINISHED with n_TFs: 86
WARNING: 4/18 Slamf7 not recoverable due to insufficient samples.
WARNING: 5/18 A630035G10Rik not recoverable due to insufficient samples.
WARNING: 6/18 Gm37065 not recoverable due to insufficient samples.
WARNING: 7/18 Fcer1a not recoverable due to insufficient samples.
Processing 8/18 Ifi206
8/18 Ifi206 FINISHED with n_TFs: 86
Processing 9/18 Ifi213
9/18 Ifi213 FINISHED with n_TFs: 86
WARNING: 10/18 Ifi207 not recoverable due to insufficient samples.
Processing 11/18 Ifi204
11/18 Ifi204 FINISHED with n_TFs: 85
WARNING: 12/18 Ifi211 not recoverable due to insufficient samples.
Processing 13/18 Ifi203
13/18 Ifi203 FINISHED with n_TFs: 86
WARNING: 14/18 Ifi205 not recoverable due to insufficient samples.
Processing 15/18 Coq8a
15/18 Coq8a FINISHED with n_TFs: 86
Processing 16/18 Cenpf
16/18 Cenpf FINISHED with n_TFs: 86
Processing 17/18 Prex2
17/18 Prex2 FINISHED with n_TFs: 86
WARNING: 0/17 Iglc2 not recoverable due to insufficient samples.
WARNING: 1/17 Gm43388 not recoverable due to insufficient samples.
WARNING: 2/17 Olfr164 not recoverable due to insufficient samples.
Processing 3/17 Klhl6
3/17 Klhl6 FINISHED with n_TFs: 86
Processing 4/17 Map6d1
4/17 Map6d1 FINISHED with n_TFs: 86
Processing 5/17 Dgkg
5/17 Dgkg FINISHED with n_TFs: 86
Processing 6/17 Parp14
6/17 Parp14 FINISHED with n_TFs: 86
WARNING: 7/17 Eaf2 not recoverable due to insufficient samples.
WARNING: 8/17 Gm36028 not recoverable due to insufficient samples.
WARNING: 9/17 Sidt1 not recoverable due to insufficient samples.
Processing 10/17 BC016579
10/17 BC016579 FINISHED with n_TFs: 86
Processing 11/17 Phldb2
11/17 Phldb2 FINISHED with n_TFs: 86
Processing 12/17 Trat1
12/17 Trat1 FINISHED with n_TFs: 86
Processing 13/17 Alcam
13/17 Alcam FINISHED with n_TFs: 86
Processing 14/17 Nfkbiz
14/17 Nfkbiz FINISHED with n_TFs: 85
WARNING: 15/17 Olfr178 not recoverable due to insufficient samples.
Processing 16/17 Samsn1
16/17 Samsn1 FINISHED with n_TFs: 86
Processing 0/17 Hp
0/17 Hp FINISHED with n_TFs: 86
Processing 1/17 Maf
1/17 Maf FINISHED with n_TFs: 85
WARNING: 2/17 Car5a not recoverable due to insufficient samples.
WARNING: 3/17 Acta1 not recoverable due to insufficient samples.
Processing 4/17 Arhgef18
4/17 Arhgef18 FINISHED with n_TFs: 86
WARNING: 5/17 Mcemp1 not recoverable due to insufficient samples.
Processing 6/17 Col4a2
6/17 Col4a2 FINISHED with n_TFs: 86
Processing 7/17 Thsd1
7/17 Thsd1 FINISHED with n_TFs: 86
Processing 8/17 Ank1
8/17 Ank1 FINISHED with n_TFs: 86
WARNING: 9/17 Gm38414 not recoverable due to insufficient samples.
WARNING: 10/17 Gpm6a not recoverable due to insufficient samples.
Processing 11/17 Ddx60
11/17 Ddx60 FINISHED with n_TFs: 86
WARNING: 12/17 March1 not recoverable due to insufficient samples.
WARNING: 13/17 Iqcn not recoverable due to insufficient samples.
Processing 14/17 Gypa
14/17 Gypa FINISHED with n_TFs: 86
Processing 15/17 Inpp4b
15/17 Inpp4b FINISHED with n_TFs: 86
Processing 16/17 Klf1
16/17 Klf1 FINISHED with n_TFs: 85
Processing 0/17 F2r
0/17 F2r FINISHED with n_TFs: 86
Processing 1/17 Ccnb1
1/17 Ccnb1 FINISHED with n_TFs: 86
Processing 2/17 Gm2822
2/17 Gm2822 FINISHED with n_TFs: 86
WARNING: 3/17 Gm48876 not recoverable due to insufficient samples.
WARNING: 4/17 Isl1 not recoverable due to insufficient samples.
WARNING: 5/17 Akr1c19 not recoverable due to insufficient samples.
Processing 6/17 Klf6
6/17 Klf6 FINISHED with n_TFs: 85
Processing 7/17 Lyst
7/17 Lyst FINISHED with n_TFs: 86
Processing 8/17 Tcrg-C1
8/17 Tcrg-C1 FINISHED with n_TFs: 86
WARNING: 9/17 Tcrg-C4 not recoverable due to insufficient samples.
Processing 10/17 Elmo1
10/17 Elmo1 FINISHED with n_TFs: 86
Processing 11/17 Cmah
11/17 Cmah FINISHED with n_TFs: 86
WARNING: 12/17 Irf4 not recoverable due to insufficient samples.
WARNING: 13/17 Gm49144 not recoverable due to insufficient samples.
Processing 14/17 Ly86
14/17 Ly86 FINISHED with n_TFs: 86
WARNING: 15/17 Bmp6 not recoverable due to insufficient samples.
Processing 16/17 Gm31834
16/17 Gm31834 FINISHED with n_TFs: 86
WARNING: 0/17 Egr2 not recoverable due to insufficient samples.
WARNING: 1/17 Derl3 not recoverable due to insufficient samples.
Processing 2/17 Vpreb3
2/17 Vpreb3 FINISHED with n_TFs: 86
Processing 3/17 Itgb2
3/17 Itgb2 FINISHED with n_TFs: 86
Processing 4/17 Prtn3
4/17 Prtn3 FINISHED with n_TFs: 86
Processing 5/17 Elane
5/17 Elane FINISHED with n_TFs: 86
WARNING: 6/17 Cfd not recoverable due to insufficient samples.
Processing 7/17 Sppl2b
7/17 Sppl2b FINISHED with n_TFs: 86
Processing 8/17 Tbxa2r
8/17 Tbxa2r FINISHED with n_TFs: 86
WARNING: 9/17 Gm16271 not recoverable due to insufficient samples.
WARNING: 10/17 1700113H08Rik not recoverable due to insufficient samples.
Processing 11/17 Igf1
11/17 Igf1 FINISHED with n_TFs: 86
WARNING: 12/17 Gm33782 not recoverable due to insufficient samples.
WARNING: 13/17 Rassf9 not recoverable due to insufficient samples.
Processing 14/17 Slc6a15
14/17 Slc6a15 FINISHED with n_TFs: 86
Processing 15/17 Osbpl8
15/17 Osbpl8 FINISHED with n_TFs: 86
Processing 16/17 Ddc
16/17 Ddc FINISHED with n_TFs: 86
Processing 0/17 Wdfy2
0/17 Wdfy2 FINISHED with n_TFs: 86
WARNING: 1/17 Gm48433 not recoverable due to insufficient samples.
Processing 2/17 Pbk
2/17 Pbk FINISHED with n_TFs: 86
WARNING: 3/17 Lgi3 not recoverable due to insufficient samples.
Processing 4/17 Dok2
4/17 Dok2 FINISHED with n_TFs: 86
WARNING: 5/17 Gfra2 not recoverable due to insufficient samples.
Processing 6/17 Rubcnl
6/17 Rubcnl FINISHED with n_TFs: 86
WARNING: 7/17 1700087I21Rik not recoverable due to insufficient samples.
Processing 8/17 Card6
8/17 Card6 FINISHED with n_TFs: 86
Processing 9/17 Il7r
9/17 Il7r FINISHED with n_TFs: 86
Processing 10/17 Gm49240
10/17 Gm49240 FINISHED with n_TFs: 86
Processing 11/17 Nipal2
11/17 Nipal2 FINISHED with n_TFs: 86
WARNING: 12/17 Gm35167 not recoverable due to insufficient samples.
Processing 13/17 Angpt1
13/17 Angpt1 FINISHED with n_TFs: 86
Processing 14/17 Trps1
14/17 Trps1 FINISHED with n_TFs: 85
WARNING: 15/17 Gm34794 not recoverable due to insufficient samples.
Processing 16/17 Samd12
16/17 Samd12 FINISHED with n_TFs: 86
Processing 0/17 Plek
0/17 Plek FINISHED with n_TFs: 86
Processing 1/17 Meis1
1/17 Meis1 FINISHED with n_TFs: 85
WARNING: 2/17 Il9r not recoverable due to insufficient samples.
Processing 3/17 Itk
3/17 Itk FINISHED with n_TFs: 86
Processing 4/17 Gm5431
4/17 Gm5431 FINISHED with n_TFs: 86
WARNING: 5/17 Zfp454 not recoverable due to insufficient samples.
WARNING: 6/17 Slc36a2 not recoverable due to insufficient samples.
WARNING: 7/17 Gjc2 not recoverable due to insufficient samples.
WARNING: 8/17 Hs3st3b1 not recoverable due to insufficient samples.
Processing 9/17 Atp1b2
9/17 Atp1b2 FINISHED with n_TFs: 86
WARNING: 10/17 Alox15 not recoverable due to insufficient samples.
Processing 11/17 Lgals9
11/17 Lgals9 FINISHED with n_TFs: 86
Processing 12/17 Ccl5
12/17 Ccl5 FINISHED with n_TFs: 86
Processing 13/17 Ccl9
13/17 Ccl9 FINISHED with n_TFs: 86
Processing 14/17 Ccl3
14/17 Ccl3 FINISHED with n_TFs: 86
Processing 15/17 Epx
15/17 Epx FINISHED with n_TFs: 86
Processing 16/17 Hlf
16/17 Hlf FINISHED with n_TFs: 85
Processing 0/17 Slc38a5
0/17 Slc38a5 FINISHED with n_TFs: 86
WARNING: 1/17 Tspan7 not recoverable due to insufficient samples.
Processing 2/17 Dock11
2/17 Dock11 FINISHED with n_TFs: 86
WARNING: 3/17 Il13ra1 not recoverable due to insufficient samples.
Processing 4/17 Gria3
4/17 Gria3 FINISHED with n_TFs: 86
Processing 5/17 Ocrl
5/17 Ocrl FINISHED with n_TFs: 86
Processing 6/17 Fhl1
6/17 Fhl1 FINISHED with n_TFs: 86
WARNING: 7/17 Fmr1nb not recoverable due to insufficient samples.
Processing 8/17 F630028O10Rik
8/17 F630028O10Rik FINISHED with n_TFs: 86
Processing 9/17 Chic1
9/17 Chic1 FINISHED with n_TFs: 86
WARNING: 10/17 Tlr13 not recoverable due to insufficient samples.
Processing 11/17 Gpr174
11/17 Gpr174 FINISHED with n_TFs: 86
Processing 12/17 Klhl4
12/17 Klhl4 FINISHED with n_TFs: 86
Processing 13/17 Nrk
13/17 Nrk FINISHED with n_TFs: 86
Processing 14/17 Pwwp3b
14/17 Pwwp3b FINISHED with n_TFs: 86
WARNING: 15/17 Rnf128 not recoverable due to insufficient samples.
WARNING: 16/17 Gm15228 not recoverable due to insufficient samples.
Processing 0/18 AC149090.1
0/18 AC149090.1 FINISHED with n_TFs: 86
Processing 1/18 Eya1
1/18 Eya1 FINISHED with n_TFs: 85
WARNING: 2/18 Gm28154 not recoverable due to insufficient samples.
WARNING: 3/18 Gm9898 not recoverable due to insufficient samples.
Processing 4/18 Bag2
4/18 Bag2 FINISHED with n_TFs: 86
Processing 5/18 Neurl3
5/18 Neurl3 FINISHED with n_TFs: 86
Processing 6/18 Lonrf2
6/18 Lonrf2 FINISHED with n_TFs: 86
Processing 7/18 Slc40a1
7/18 Slc40a1 FINISHED with n_TFs: 86
WARNING: 8/18 C2cd6 not recoverable due to insufficient samples.
Processing 9/18 Mpp4
9/18 Mpp4 FINISHED with n_TFs: 86
WARNING: 10/18 Gm4208 not recoverable due to insufficient samples.
Processing 11/18 Idh1
11/18 Idh1 FINISHED with n_TFs: 86
Processing 12/18 Obsl1
12/18 Obsl1 FINISHED with n_TFs: 86
Processing 13/18 Serpine2
13/18 Serpine2 FINISHED with n_TFs: 86
WARNING: 14/18 Pid1 not recoverable due to insufficient samples.
WARNING: 15/18 Gpr55 not recoverable due to insufficient samples.
WARNING: 16/18 Pdcd1 not recoverable due to insufficient samples.
Processing 17/18 St8sia4
17/18 St8sia4 FINISHED with n_TFs: 86
Processing 0/18 Pacc1
0/18 Pacc1 FINISHED with n_TFs: 86
Processing 1/18 Phactr2
1/18 Phactr2 FINISHED with n_TFs: 86
Processing 2/18 Slc35d3
2/18 Slc35d3 FINISHED with n_TFs: 86
Processing 3/18 Myb
3/18 Myb FINISHED with n_TFs: 85
WARNING: 4/18 Platr6 not recoverable due to insufficient samples.
Processing 5/18 Eya4
5/18 Eya4 FINISHED with n_TFs: 85
Processing 6/18 Arg1
6/18 Arg1 FINISHED with n_TFs: 86
WARNING: 7/18 Prdm1 not recoverable due to insufficient samples.
Processing 8/18 Man1a
8/18 Man1a FINISHED with n_TFs: 86
WARNING: 9/18 Oit3 not recoverable due to insufficient samples.
WARNING: 10/18 Chst3 not recoverable due to insufficient samples.
Processing 11/18 Cdk1
11/18 Cdk1 FINISHED with n_TFs: 86
Processing 12/18 Ncln
12/18 Ncln FINISHED with n_TFs: 86
Processing 13/18 Zfp938
13/18 Zfp938 FINISHED with n_TFs: 86
Processing 14/18 Hsp90b1
14/18 Hsp90b1 FINISHED with n_TFs: 86
WARNING: 15/18 Stab2 not recoverable due to insufficient samples.
WARNING: 16/18 Nr1h4 not recoverable due to insufficient samples.
WARNING: 17/18 Slc17a8 not recoverable due to insufficient samples.
Processing 0/17 Phf11a
0/17 Phf11a FINISHED with n_TFs: 86
Processing 1/17 Phf11b
1/17 Phf11b FINISHED with n_TFs: 86
WARNING: 2/17 Tnfrsf19 not recoverable due to insufficient samples.
Processing 3/17 Fdft1
3/17 Fdft1 FINISHED with n_TFs: 86
WARNING: 4/17 Blk not recoverable due to insufficient samples.
WARNING: 5/17 Gm15918 not recoverable due to insufficient samples.
Processing 6/17 Fndc3a
6/17 Fndc3a FINISHED with n_TFs: 86
Processing 7/17 Rgcc
7/17 Rgcc FINISHED with n_TFs: 86
Processing 8/17 Diaph3
8/17 Diaph3 FINISHED with n_TFs: 86
WARNING: 9/17 Gm27198 not recoverable due to insufficient samples.
Processing 10/17 Zmiz1
10/17 Zmiz1 FINISHED with n_TFs: 86
Processing 11/17 Arhgef3
11/17 Arhgef3 FINISHED with n_TFs: 86
Processing 12/17 Lgals3
12/17 Lgals3 FINISHED with n_TFs: 86
WARNING: 13/17 Rnase10 not recoverable due to insufficient samples.
Processing 14/17 Olfr1509
14/17 Olfr1509 FINISHED with n_TFs: 86
WARNING: 15/17 Trav16d-dv11 not recoverable due to insufficient samples.
Processing 16/17 Shisa2
16/17 Shisa2 FINISHED with n_TFs: 86
WARNING: 0/17 Olfr1258 not recoverable due to insufficient samples.
WARNING: 1/17 Chst1 not recoverable due to insufficient samples.
Processing 2/17 Gm10801
2/17 Gm10801 FINISHED with n_TFs: 86
Processing 3/17 Slc12a6
3/17 Slc12a6 FINISHED with n_TFs: 86
Processing 4/17 Thbs1
4/17 Thbs1 FINISHED with n_TFs: 86
Processing 5/17 Bub1b
5/17 Bub1b FINISHED with n_TFs: 86
Processing 6/17 Spint1
6/17 Spint1 FINISHED with n_TFs: 86
WARNING: 7/17 Dll4 not recoverable due to insufficient samples.
Processing 8/17 Nusap1
8/17 Nusap1 FINISHED with n_TFs: 86
WARNING: 9/17 4930417H01Rik not recoverable due to insufficient samples.
WARNING: 10/17 Sema6d not recoverable due to insufficient samples.
WARNING: 11/17 Gpat2 not recoverable due to insufficient samples.
Processing 12/17 Atrn
12/17 Atrn FINISHED with n_TFs: 86
Processing 13/17 Cdc25b
13/17 Cdc25b FINISHED with n_TFs: 86
Processing 14/17 Rin2
14/17 Rin2 FINISHED with n_TFs: 86
Processing 15/17 Cst7
15/17 Cst7 FINISHED with n_TFs: 86
Processing 16/17 Slc52a3
16/17 Slc52a3 FINISHED with n_TFs: 86
Processing 0/17 Cyld
0/17 Cyld FINISHED with n_TFs: 86
WARNING: 1/17 Slc12a3 not recoverable due to insufficient samples.
Processing 2/17 Herpud1
2/17 Herpud1 FINISHED with n_TFs: 86
Processing 3/17 Adgrg3
3/17 Adgrg3 FINISHED with n_TFs: 86
Processing 4/17 Ces2g
4/17 Ces2g FINISHED with n_TFs: 86
WARNING: 5/17 Cdh1 not recoverable due to insufficient samples.
Processing 6/17 Plcg2
6/17 Plcg2 FINISHED with n_TFs: 86
Processing 7/17 Irf8
7/17 Irf8 FINISHED with n_TFs: 85
Processing 8/17 Def8
8/17 Def8 FINISHED with n_TFs: 86
WARNING: 9/17 Amotl1 not recoverable due to insufficient samples.
WARNING: 10/17 Piwil4 not recoverable due to insufficient samples.
Processing 11/17 Aplp2
11/17 Aplp2 FINISHED with n_TFs: 86
WARNING: 12/17 Kcnj5 not recoverable due to insufficient samples.
WARNING: 13/17 Crtam not recoverable due to insufficient samples.
Processing 14/17 Hmbs
14/17 Hmbs FINISHED with n_TFs: 86
Processing 15/17 Il10ra
15/17 Il10ra FINISHED with n_TFs: 86
Processing 16/17 Zbtb16
16/17 Zbtb16 FINISHED with n_TFs: 85
WARNING: 0/17 Fbxo39 not recoverable due to insufficient samples.
Processing 1/17 P2rx1
1/17 P2rx1 FINISHED with n_TFs: 86
Processing 2/17 Rtn4rl1
2/17 Rtn4rl1 FINISHED with n_TFs: 86
Processing 3/17 Rilp
3/17 Rilp FINISHED with n_TFs: 86
Processing 4/17 Scarf1
4/17 Scarf1 FINISHED with n_TFs: 86
Processing 5/17 Slc43a2
5/17 Slc43a2 FINISHED with n_TFs: 86
WARNING: 6/17 Rskr not recoverable due to insufficient samples.
Processing 7/17 Rab11fip4
7/17 Rab11fip4 FINISHED with n_TFs: 86
WARNING: 8/17 Tmem132e not recoverable due to insufficient samples.
Processing 9/17 Ccl4
9/17 Ccl4 FINISHED with n_TFs: 86
Processing 10/17 Wfdc17
10/17 Wfdc17 FINISHED with n_TFs: 86
Processing 11/17 Tspoap1
11/17 Tspoap1 FINISHED with n_TFs: 86
Processing 12/17 Mpo
12/17 Mpo FINISHED with n_TFs: 86
WARNING: 13/17 Skap1 not recoverable due to insufficient samples.
Processing 14/17 Itgb3
14/17 Itgb3 FINISHED with n_TFs: 86
WARNING: 15/17 Mrc2 not recoverable due to insufficient samples.
Processing 16/17 Tanc2
16/17 Tanc2 FINISHED with n_TFs: 86
Processing 0/17 Fam169b
0/17 Fam169b FINISHED with n_TFs: 86
Processing 1/17 Rab38
1/17 Rab38 FINISHED with n_TFs: 86
Processing 2/17 Gdpd5
2/17 Gdpd5 FINISHED with n_TFs: 86
Processing 3/17 Pde2a
3/17 Pde2a FINISHED with n_TFs: 86
Processing 4/17 Rrm1
4/17 Rrm1 FINISHED with n_TFs: 86
WARNING: 5/17 Olfr65 not recoverable due to insufficient samples.
WARNING: 6/17 Olfr632 not recoverable due to insufficient samples.
Processing 7/17 Trim6
7/17 Trim6 FINISHED with n_TFs: 86
WARNING: 8/17 Olfr657 not recoverable due to insufficient samples.
Processing 9/17 Ppfibp2
9/17 Ppfibp2 FINISHED with n_TFs: 86
Processing 10/17 Ctr9
10/17 Ctr9 FINISHED with n_TFs: 85
Processing 11/17 Mical2
11/17 Mical2 FINISHED with n_TFs: 86
WARNING: 12/17 A730082K24Rik not recoverable due to insufficient samples.
WARNING: 13/17 Gm34225 not recoverable due to insufficient samples.
Processing 14/17 Nucb2
14/17 Nucb2 FINISHED with n_TFs: 86
Processing 15/17 Plk1
15/17 Plk1 FINISHED with n_TFs: 86
Processing 16/17 Itgam
16/17 Itgam FINISHED with n_TFs: 86
Processing 0/17 Stxbp4
0/17 Stxbp4 FINISHED with n_TFs: 86
Processing 1/17 Arl5c
1/17 Arl5c FINISHED with n_TFs: 86
WARNING: 2/17 Stac2 not recoverable due to insufficient samples.
WARNING: 3/17 Ikzf3 not recoverable due to insufficient samples.
Processing 4/17 Top2a
4/17 Top2a FINISHED with n_TFs: 86
WARNING: 5/17 Krt222 not recoverable due to insufficient samples.
WARNING: 6/17 Hap1 not recoverable due to insufficient samples.
Processing 7/17 Stat3
7/17 Stat3 FINISHED with n_TFs: 85
WARNING: 8/17 Slc4a1 not recoverable due to insufficient samples.
Processing 9/17 Itga2b
9/17 Itga2b FINISHED with n_TFs: 86
Processing 10/17 Cd79b
10/17 Cd79b FINISHED with n_TFs: 86
Processing 11/17 Pecam1
11/17 Pecam1 FINISHED with n_TFs: 86
Processing 12/17 Kpna2
12/17 Kpna2 FINISHED with n_TFs: 85
Processing 13/17 Pitpnc1
13/17 Pitpnc1 FINISHED with n_TFs: 86
WARNING: 14/17 Abca9 not recoverable due to insufficient samples.
Processing 15/17 Abca5
15/17 Abca5 FINISHED with n_TFs: 86
Processing 16/17 2610035D17Rik
16/17 2610035D17Rik FINISHED with n_TFs: 86
WARNING: 0/17 Lrg1 not recoverable due to insufficient samples.
Processing 1/17 Dennd1c
1/17 Dennd1c FINISHED with n_TFs: 86
WARNING: 2/17 Pdzph1 not recoverable due to insufficient samples.
Processing 3/17 Rab31
3/17 Rab31 FINISHED with n_TFs: 86
Processing 4/17 Nlrc4
4/17 Nlrc4 FINISHED with n_TFs: 86
Processing 5/17 Nrxn1
5/17 Nrxn1 FINISHED with n_TFs: 86
Processing 6/17 Zdhhc14
6/17 Zdhhc14 FINISHED with n_TFs: 86
WARNING: 7/17 Ccr6 not recoverable due to insufficient samples.
WARNING: 8/17 Pde10a not recoverable due to insufficient samples.
WARNING: 9/17 Prss34 not recoverable due to insufficient samples.
Processing 10/17 Cdkn1a
10/17 Cdkn1a FINISHED with n_TFs: 86
Processing 11/17 Rab44
11/17 Rab44 FINISHED with n_TFs: 86
Processing 12/17 Fgd2
12/17 Fgd2 FINISHED with n_TFs: 86
Processing 13/17 Myo1f
13/17 Myo1f FINISHED with n_TFs: 86
Processing 14/17 H2-DMb2
14/17 H2-DMb2 FINISHED with n_TFs: 86
Processing 15/17 H2-Ab1
15/17 H2-Ab1 FINISHED with n_TFs: 86
Processing 16/17 Ltb
16/17 Ltb FINISHED with n_TFs: 86
Processing 0/17 Ifit3
0/17 Ifit3 FINISHED with n_TFs: 86
Processing 1/17 Kif11
1/17 Kif11 FINISHED with n_TFs: 86
Processing 2/17 Dntt
2/17 Dntt FINISHED with n_TFs: 86
WARNING: 3/17 Abcc2 not recoverable due to insufficient samples.
Processing 4/17 Optn
4/17 Optn FINISHED with n_TFs: 86
Processing 5/17 Gata3
5/17 Gata3 FINISHED with n_TFs: 85
Processing 6/17 St8sia6
6/17 St8sia6 FINISHED with n_TFs: 86
WARNING: 7/17 Cacna1b not recoverable due to insufficient samples.
Processing 8/17 Lcn12
8/17 Lcn12 FINISHED with n_TFs: 86
WARNING: 9/17 Sohlh1 not recoverable due to insufficient samples.
Processing 10/17 Lcn4
10/17 Lcn4 FINISHED with n_TFs: 86
WARNING: 11/17 Fcnb not recoverable due to insufficient samples.
Processing 12/17 Gfi1b
12/17 Gfi1b FINISHED with n_TFs: 85
Processing 13/17 Ggta1
13/17 Ggta1 FINISHED with n_TFs: 86
Processing 14/17 Cytip
14/17 Cytip FINISHED with n_TFs: 86
Processing 15/17 Baz2b
15/17 Baz2b FINISHED with n_TFs: 86
WARNING: 16/17 Zswim2 not recoverable due to insufficient samples.
Processing 0/17 Tpx2
0/17 Tpx2 FINISHED with n_TFs: 86
WARNING: 1/17 Xkr7 not recoverable due to insufficient samples.
Processing 2/17 Hck
2/17 Hck FINISHED with n_TFs: 86
Processing 3/17 Procr
3/17 Procr FINISHED with n_TFs: 86
WARNING: 4/17 Tox2 not recoverable due to insufficient samples.
Processing 5/17 Ube2c
5/17 Ube2c FINISHED with n_TFs: 86
Processing 6/17 Mmp9
6/17 Mmp9 FINISHED with n_TFs: 85
WARNING: 7/17 Cd40 not recoverable due to insufficient samples.
Processing 8/17 Eya2
8/17 Eya2 FINISHED with n_TFs: 85
WARNING: 9/17 Dok5 not recoverable due to insufficient samples.
WARNING: 10/17 Edn3 not recoverable due to insufficient samples.
Processing 11/17 Slco4a1
11/17 Slco4a1 FINISHED with n_TFs: 86
Processing 12/17 Car1
12/17 Car1 FINISHED with n_TFs: 86
Processing 13/17 Cyp7b1
13/17 Cyp7b1 FINISHED with n_TFs: 86
Processing 14/17 Cpa3
14/17 Cpa3 FINISHED with n_TFs: 86
Processing 15/17 Fndc3b
15/17 Fndc3b FINISHED with n_TFs: 86
Processing 16/17 Mecom
16/17 Mecom FINISHED with n_TFs: 85
Processing 0/17 Ciita
0/17 Ciita FINISHED with n_TFs: 85
WARNING: 1/17 Tnfrsf17 not recoverable due to insufficient samples.
Processing 2/17 Shisa9
2/17 Shisa9 FINISHED with n_TFs: 86
WARNING: 3/17 St6gal1 not recoverable due to insufficient samples.
Processing 4/17 Rtp4
4/17 Rtp4 FINISHED with n_TFs: 86
Processing 5/17 Lpp
5/17 Lpp FINISHED with n_TFs: 86
WARNING: 6/17 Gm46560 not recoverable due to insufficient samples.
Processing 7/17 Tfrc
7/17 Tfrc FINISHED with n_TFs: 86
Processing 8/17 Muc13
8/17 Muc13 FINISHED with n_TFs: 86
Processing 9/17 Mylk
9/17 Mylk FINISHED with n_TFs: 86
WARNING: 10/17 Ildr1 not recoverable due to insufficient samples.
Processing 11/17 Zbtb20
11/17 Zbtb20 FINISHED with n_TFs: 85
Processing 12/17 Cd200r1
12/17 Cd200r1 FINISHED with n_TFs: 86
Processing 13/17 Retnlg
13/17 Retnlg FINISHED with n_TFs: 86
Processing 14/17 Gbe1
14/17 Gbe1 FINISHED with n_TFs: 86
WARNING: 15/17 Ncam2 not recoverable due to insufficient samples.
Processing 16/17 Jam2
16/17 Jam2 FINISHED with n_TFs: 86
Processing 0/17 Ctsw
0/17 Ctsw FINISHED with n_TFs: 86
WARNING: 1/17 9830166K06Rik not recoverable due to insufficient samples.
Processing 2/17 Cd6
2/17 Cd6 FINISHED with n_TFs: 86
WARNING: 3/17 Ms4a6d not recoverable due to insufficient samples.
Processing 4/17 Ms4a2
4/17 Ms4a2 FINISHED with n_TFs: 86
Processing 5/17 Ms4a3
5/17 Ms4a3 FINISHED with n_TFs: 86
WARNING: 6/17 Oosp1 not recoverable due to insufficient samples.
Processing 7/17 Gda
7/17 Gda FINISHED with n_TFs: 86
Processing 8/17 Mamdc2
8/17 Mamdc2 FINISHED with n_TFs: 86
Processing 9/17 Glis3
9/17 Glis3 FINISHED with n_TFs: 85
Processing 10/17 Prkg1
10/17 Prkg1 FINISHED with n_TFs: 86
Processing 11/17 Asah2
11/17 Asah2 FINISHED with n_TFs: 86
Processing 12/17 Sgms1
12/17 Sgms1 FINISHED with n_TFs: 86
WARNING: 13/17 Ankrd22 not recoverable due to insufficient samples.
WARNING: 14/17 Acta2 not recoverable due to insufficient samples.
Processing 15/17 Ifit1bl1
15/17 Ifit1bl1 FINISHED with n_TFs: 86
Processing 16/17 Slc16a12
16/17 Slc16a12 FINISHED with n_TFs: 86
Processing 0/17 Fam171a1
0/17 Fam171a1 FINISHED with n_TFs: 86
Processing 1/17 Fam107b
1/17 Fam107b FINISHED with n_TFs: 86
Processing 2/17 Itih5
2/17 Itih5 FINISHED with n_TFs: 86
Processing 3/17 Prkcq
3/17 Prkcq FINISHED with n_TFs: 86
WARNING: 4/17 Il2ra not recoverable due to insufficient samples.
Processing 5/17 Vim
5/17 Vim FINISHED with n_TFs: 86
Processing 6/17 Plxdc2
6/17 Plxdc2 FINISHED with n_TFs: 86
WARNING: 7/17 Adamtsl2 not recoverable due to insufficient samples.
WARNING: 8/17 Pip5kl1 not recoverable due to insufficient samples.
Processing 9/17 Eng
9/17 Eng FINISHED with n_TFs: 86
Processing 10/17 Ptgs1
10/17 Ptgs1 FINISHED with n_TFs: 86
Processing 11/17 Kynu
11/17 Kynu FINISHED with n_TFs: 86
Processing 12/17 Fmnl2
12/17 Fmnl2 FINISHED with n_TFs: 86
Processing 13/17 Itga6
13/17 Itga6 FINISHED with n_TFs: 86
Processing 14/17 Fam171b
14/17 Fam171b FINISHED with n_TFs: 86
WARNING: 15/17 Prg2 not recoverable due to insufficient samples.
WARNING: 16/17 Prg3 not recoverable due to insufficient samples.
Processing 0/17 Myl10
0/17 Myl10 FINISHED with n_TFs: 86
WARNING: 1/17 Cldn15 not recoverable due to insufficient samples.
WARNING: 2/17 Hepacam2 not recoverable due to insufficient samples.
WARNING: 3/17 Pdk4 not recoverable due to insufficient samples.
Processing 4/17 Asns
4/17 Asns FINISHED with n_TFs: 86
WARNING: 5/17 A430035B10Rik not recoverable due to insufficient samples.
Processing 6/17 Tspan12
6/17 Tspan12 FINISHED with n_TFs: 86
Processing 7/17 Cadps2
7/17 Cadps2 FINISHED with n_TFs: 86
Processing 8/17 Slc23a4
8/17 Slc23a4 FINISHED with n_TFs: 86
Processing 9/17 Kel
9/17 Kel FINISHED with n_TFs: 86
Processing 10/17 Pdia4
10/17 Pdia4 FINISHED with n_TFs: 86
Processing 11/17 Gimap6
11/17 Gimap6 FINISHED with n_TFs: 86
Processing 12/17 Gimap3
12/17 Gimap3 FINISHED with n_TFs: 86
Processing 13/17 Skap2
13/17 Skap2 FINISHED with n_TFs: 86
Processing 14/17 Hoxa9
14/17 Hoxa9 FINISHED with n_TFs: 85
WARNING: 15/17 Cpvl not recoverable due to insufficient samples.
Processing 16/17 Scrn1
16/17 Scrn1 FINISHED with n_TFs: 86
Processing 0/17 Il12a
0/17 Il12a FINISHED with n_TFs: 86
WARNING: 1/17 Pdgfc not recoverable due to insufficient samples.
Processing 2/17 Tmem154
2/17 Tmem154 FINISHED with n_TFs: 86
WARNING: 3/17 Fcrl5 not recoverable due to insufficient samples.
Processing 4/17 Sh2d2a
4/17 Sh2d2a FINISHED with n_TFs: 86
Processing 5/17 Fam189b
5/17 Fam189b FINISHED with n_TFs: 86
Processing 6/17 Muc1
6/17 Muc1 FINISHED with n_TFs: 86
Processing 7/17 S100a4
7/17 S100a4 FINISHED with n_TFs: 86
Processing 8/17 S100a8
8/17 S100a8 FINISHED with n_TFs: 86
Processing 9/17 Ctss
9/17 Ctss FINISHED with n_TFs: 86
WARNING: 10/17 Ppm1j not recoverable due to insufficient samples.
Processing 11/17 Sort1
11/17 Sort1 FINISHED with n_TFs: 86
Processing 12/17 Arhgap29
12/17 Arhgap29 FINISHED with n_TFs: 86
WARNING: 13/17 Bcar3 not recoverable due to insufficient samples.
Processing 14/17 Camk2d
14/17 Camk2d FINISHED with n_TFs: 86
WARNING: 15/17 Lef1 not recoverable due to insufficient samples.
Processing 16/17 Cenpe
16/17 Cenpe FINISHED with n_TFs: 86
Processing 0/17 Sdc1
0/17 Sdc1 FINISHED with n_TFs: 86
Processing 1/17 Rrm2
1/17 Rrm2 FINISHED with n_TFs: 86
WARNING: 2/17 Gm36723 not recoverable due to insufficient samples.
WARNING: 3/17 Slc26a3 not recoverable due to insufficient samples.
Processing 4/17 Prkch
4/17 Prkch FINISHED with n_TFs: 86
Processing 5/17 Rhoj
5/17 Rhoj FINISHED with n_TFs: 86
Processing 6/17 Mthfd1
6/17 Mthfd1 FINISHED with n_TFs: 86
Processing 7/17 Akap5
7/17 Akap5 FINISHED with n_TFs: 86
Processing 8/17 Fut8
8/17 Fut8 FINISHED with n_TFs: 86
Processing 9/17 Sipa1l1
9/17 Sipa1l1 FINISHED with n_TFs: 86
Processing 10/17 Fos
10/17 Fos FINISHED with n_TFs: 85
Processing 11/17 Serpina3g
11/17 Serpina3g FINISHED with n_TFs: 86
WARNING: 12/17 B830012L14Rik not recoverable due to insufficient samples.
WARNING: 13/17 Amn not recoverable due to insufficient samples.
WARNING: 14/17 Gm36635 not recoverable due to insufficient samples.
Processing 15/17 Pld4
15/17 Pld4 FINISHED with n_TFs: 86
Processing 16/17 Crip2
16/17 Crip2 FINISHED with n_TFs: 86
Processing 0/17 Ttc39b
0/17 Ttc39b FINISHED with n_TFs: 86
WARNING: 1/17 Slc24a2 not recoverable due to insufficient samples.
Processing 2/17 Mllt3
2/17 Mllt3 FINISHED with n_TFs: 85
Processing 3/17 Hacd4
3/17 Hacd4 FINISHED with n_TFs: 86
Processing 4/17 Cyp2j6
4/17 Cyp2j6 FINISHED with n_TFs: 86
Processing 5/17 Cyp2j9
5/17 Cyp2j9 FINISHED with n_TFs: 86
Processing 6/17 Prkaa2
6/17 Prkaa2 FINISHED with n_TFs: 86
WARNING: 7/17 Mroh7 not recoverable due to insufficient samples.
Processing 8/17 Cdc20
8/17 Cdc20 FINISHED with n_TFs: 86
Processing 9/17 Mpl
9/17 Mpl FINISHED with n_TFs: 86
Processing 10/17 Tie1
10/17 Tie1 FINISHED with n_TFs: 86
Processing 11/17 Ermap
11/17 Ermap FINISHED with n_TFs: 86
WARNING: 12/17 Bmp8a not recoverable due to insufficient samples.
WARNING: 13/17 Maneal not recoverable due to insufficient samples.
Processing 14/17 Cdca8
14/17 Cdca8 FINISHED with n_TFs: 86
Processing 15/17 Gjb3
15/17 Gjb3 FINISHED with n_TFs: 86
WARNING: 16/17 Hcrtr1 not recoverable due to insufficient samples.
Processing 0/18 Amdhd1
0/18 Amdhd1 FINISHED with n_TFs: 86
Processing 1/18 Gm15915
1/18 Gm15915 FINISHED with n_TFs: 86
Processing 2/18 Plxnc1
2/18 Plxnc1 FINISHED with n_TFs: 86
Processing 3/18 Rap1b
3/18 Rap1b FINISHED with n_TFs: 86
WARNING: 4/18 Gm47425 not recoverable due to insufficient samples.
Processing 5/18 Irak3
5/18 Irak3 FINISHED with n_TFs: 86
WARNING: 6/18 Gpr182 not recoverable due to insufficient samples.
Processing 7/18 Dgka
7/18 Dgka FINISHED with n_TFs: 86
Processing 8/18 Plekhg1
8/18 Plekhg1 FINISHED with n_TFs: 86
Processing 9/18 Esr1
9/18 Esr1 FINISHED with n_TFs: 85
Processing 10/18 Il22ra2
10/18 Il22ra2 FINISHED with n_TFs: 86
WARNING: 11/18 Samd3 not recoverable due to insufficient samples.
WARNING: 12/18 Themis not recoverable due to insufficient samples.
Processing 13/18 Cdk19
13/18 Cdk19 FINISHED with n_TFs: 86
Processing 14/18 Scml4
14/18 Scml4 FINISHED with n_TFs: 86
WARNING: 15/18 1700027J07Rik not recoverable due to insufficient samples.
WARNING: 16/18 4933404K13Rik not recoverable due to insufficient samples.
Processing 17/18 Pbld1
17/18 Pbld1 FINISHED with n_TFs: 86
Processing 0/17 Tmem176a
0/17 Tmem176a FINISHED with n_TFs: 86
Processing 1/17 Creb5
1/17 Creb5 FINISHED with n_TFs: 85
Processing 2/17 Aqp1
2/17 Aqp1 FINISHED with n_TFs: 86
Processing 3/17 Herc6
3/17 Herc6 FINISHED with n_TFs: 86
Processing 4/17 Mmrn1
4/17 Mmrn1 FINISHED with n_TFs: 86
Processing 5/17 Tnip3
5/17 Tnip3 FINISHED with n_TFs: 86
Processing 6/17 Ndnf
6/17 Ndnf FINISHED with n_TFs: 86
Processing 7/17 Gng12
7/17 Gng12 FINISHED with n_TFs: 86
Processing 8/17 Igkv1-135
8/17 Igkv1-135 FINISHED with n_TFs: 86
WARNING: 9/17 Igkv14-130 not recoverable due to insufficient samples.
WARNING: 10/17 Igkv1-110 not recoverable due to insufficient samples.
WARNING: 11/17 Igkv3-10 not recoverable due to insufficient samples.
Processing 12/17 Igkv3-9
12/17 Igkv3-9 FINISHED with n_TFs: 86
WARNING: 13/17 Gm30211 not recoverable due to insufficient samples.
WARNING: 14/17 1700003E16Rik not recoverable due to insufficient samples.
Processing 15/17 Efcc1
15/17 Efcc1 FINISHED with n_TFs: 86
Processing 16/17 Gp9
16/17 Gp9 FINISHED with n_TFs: 86
WARNING: 0/17 Klre1 not recoverable due to insufficient samples.
Processing 1/17 Klrd1
1/17 Klrd1 FINISHED with n_TFs: 86
Processing 2/17 Etv6
2/17 Etv6 FINISHED with n_TFs: 85
Processing 3/17 Emp1
3/17 Emp1 FINISHED with n_TFs: 86
WARNING: 4/17 Pde3a not recoverable due to insufficient samples.
WARNING: 5/17 4930479D17Rik not recoverable due to insufficient samples.
WARNING: 6/17 Arntl2 not recoverable due to insufficient samples.
WARNING: 7/17 Far2 not recoverable due to insufficient samples.
Processing 8/17 Pirb
8/17 Pirb FINISHED with n_TFs: 86
Processing 9/17 Lair1
9/17 Lair1 FINISHED with n_TFs: 86
Processing 10/17 Fosb
10/17 Fosb FINISHED with n_TFs: 85
Processing 11/17 Bloc1s3
11/17 Bloc1s3 FINISHED with n_TFs: 86
Processing 12/17 Relb
12/17 Relb FINISHED with n_TFs: 85
Processing 13/17 Apoe
13/17 Apoe FINISHED with n_TFs: 86
Processing 14/17 Atp1a3
14/17 Atp1a3 FINISHED with n_TFs: 86
Processing 15/17 Ccne1
15/17 Ccne1 FINISHED with n_TFs: 86
Processing 16/17 Cd33
16/17 Cd33 FINISHED with n_TFs: 86
WARNING: 0/17 Fxyd6 not recoverable due to insufficient samples.
WARNING: 1/17 Pou2af1 not recoverable due to insufficient samples.
Processing 2/17 Cyp11a1
2/17 Cyp11a1 FINISHED with n_TFs: 86
Processing 3/17 Hexa
3/17 Hexa FINISHED with n_TFs: 86
WARNING: 4/17 Gm33699 not recoverable due to insufficient samples.
Processing 5/17 Rora
5/17 Rora FINISHED with n_TFs: 85
Processing 6/17 Anxa2
6/17 Anxa2 FINISHED with n_TFs: 86
Processing 7/17 Fam214a
7/17 Fam214a FINISHED with n_TFs: 86
Processing 8/17 Myo5c
8/17 Myo5c FINISHED with n_TFs: 86
Processing 9/17 Ctsh
9/17 Ctsh FINISHED with n_TFs: 86
Processing 10/17 Plscr4
10/17 Plscr4 FINISHED with n_TFs: 86
Processing 11/17 Slc9a9
11/17 Slc9a9 FINISHED with n_TFs: 86
Processing 12/17 Uba7
12/17 Uba7 FINISHED with n_TFs: 86
WARNING: 13/17 Plxnb1 not recoverable due to insufficient samples.
Processing 14/17 Ngp
14/17 Ngp FINISHED with n_TFs: 86
Processing 15/17 Ltf
15/17 Ltf FINISHED with n_TFs: 86
WARNING: 16/17 Dlec1 not recoverable due to insufficient samples.
Processing 0/18 Fam129a
0/18 Fam129a FINISHED with n_TFs: 86
Processing 1/18 Glul
1/18 Glul FINISHED with n_TFs: 86
WARNING: 2/18 Sele not recoverable due to insufficient samples.
Processing 3/18 Sell
3/18 Sell FINISHED with n_TFs: 86
Processing 4/18 Selp
4/18 Selp FINISHED with n_TFs: 86
Processing 5/18 Arhgap30
5/18 Arhgap30 FINISHED with n_TFs: 86
Processing 6/18 F11r
6/18 F11r FINISHED with n_TFs: 86
Processing 7/18 Cd48
7/18 Cd48 FINISHED with n_TFs: 86
Processing 8/18 Slamf1
8/18 Slamf1 FINISHED with n_TFs: 86
Processing 9/18 Cd84
9/18 Cd84 FINISHED with n_TFs: 86
WARNING: 10/18 Slamf6 not recoverable due to insufficient samples.
WARNING: 11/18 Slamf9 not recoverable due to insufficient samples.
Processing 12/18 Ifi209
12/18 Ifi209 FINISHED with n_TFs: 86
Processing 13/18 Ifi208
13/18 Ifi208 FINISHED with n_TFs: 86
WARNING: 14/18 Gm37306 not recoverable due to insufficient samples.
WARNING: 15/18 Catspere1 not recoverable due to insufficient samples.
Processing 16/18 Kif26b
16/18 Kif26b FINISHED with n_TFs: 86
WARNING: 17/18 Batf3 not recoverable due to insufficient samples.
    finished (2:49:59) --> added 
    'fit_pars', fitted parameters for splicing dynamics (adata.var)

grn_estimate = pd.DataFrame(0, index=adata.var_names, columns=adata.var_names)
grn_estimate.loc[:, TF] = adata.varm["fit_weights_final"]
grn_estimate = np.array(grn_estimate)

grn_estimate = np.abs(grn_estimate)

grn_estimate = pd.DataFrame(grn_estimate, index=adata.var_names.tolist(), columns=adata.var_names.tolist())

grn_estimate = grn_estimate.loc[:, TF].copy()

grn = pd.DataFrame(grn_estimate.stack()).reset_index()
grn.columns = ["Gene2", "Gene1", "EdgeWeight"]

result = grn[["Gene1", "Gene2", "EdgeWeight"]].sort_values(by="EdgeWeight", ascending=False).reset_index(drop=True)

WARNING: 0/17 Olfr523 not recoverable due to insufficient samples.
Processing 1/17 Ifitm1
1/17 Ifitm1 FINISHED with n_TFs: 86
WARNING: 2/17 Muc5ac not recoverable due to insufficient samples.
Processing 3/17 Lsp1
3/17 Lsp1 FINISHED with n_TFs: 86
Processing 4/17 Fgf3
4/17 Fgf3 FINISHED with n_TFs: 86
WARNING: 5/17 Cd209a not recoverable due to insufficient samples.
Processing 6/17 Rasa3
6/17 Rasa3 FINISHED with n_TFs: 86
Processing 7/17 Rbpms
7/17 Rbpms FINISHED with n_TFs: 86
Processing 8/17 Mtus1
8/17 Mtus1 FINISHED with n_TFs: 86
Processing 9/17 Tlr3
9/17 Tlr3 FINISHED with n_TFs: 86
Processing 10/17 Palld
10/17 Palld FINISHED with n_TFs: 86
Processing 11/17 Csgalnact1
11/17 Csgalnact1 FINISHED with n_TFs: 86
Processing 12/17 Slc18a1
12/17 Slc18a1 FINISHED with n_TFs: 86
WARNING: 13/17 Cilp2 not recoverable due to insufficient samples.
Processing 14/17 Ifi30
14/17 Ifi30 FINISHED with n_TFs: 86
Processing 15/17 Cyp4f18
15/17 Cyp4f18 FINISHED with n_TFs: 86
Processing 16/17 Calr
16/17 Calr FINISHED with n_TFs: 86

Load ground truth GRN

gt = pd.read_csv(DATA_DIR / DATASET / "raw" / "mHSC-ChIP-seq-network.csv")

gt["Gene1"] = [i[0].upper() + i[1:].lower() for i in gt["Gene1"].tolist()]
gt["Gene2"] = [i[0].upper() + i[1:].lower() for i in gt["Gene2"].tolist()]
gt = gt.loc[[i in TF for i in gt["Gene1"]], :]
gt = gt.loc[[i in adata.var_names for i in gt["Gene2"]], :]
gt

	Gene1	Gene2	Score
24829	Bcl11b	Ccna2	2546.0
24913	Bcl11b	Edem1	2532.0
24928	Bcl11b	Tmem229b	2023.0
25015	Bcl11b	Clptm1l	1598.0
25037	Bcl11b	Cyld	2156.0
...	...	...	...
942678	Stat3	Abcg3	101.0
942681	Stat3	Il10	607.0
942686	Stat3	Arg1	499.0
942696	Stat3	Mmp9	445.0
942698	Stat3	Cd209a	437.0

8940 rows × 3 columns

Result

_, _, EPR_score = unsigned(gt, result)

EPR: 1.1168781625012503

AUC_score = calculate_auroc(result, gt)

result_df = pd.DataFrame({"EPR": EPR_score, "AUC": AUC_score, "Method": ["tfvelo"]})

if SAVE_DATA:
    result_df.to_csv(DATA_DIR / DATASET / "results" / "GRN_benchmark_tfv.csv")