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swolock / scrublet

Detect doublets in single-cell RNA-seq data
MIT License
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scrublet doesn't work properly #28

Open huwenrime opened 3 years ago

huwenrime commented 3 years ago

Scrublet is installed normally, but cannot run....

Python 3.8.5 (default, Sep 4 2020, 07:30:14) [GCC 7.3.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.

import scrublet import scrublet as scr import scipy.io import matplotlib.pyplot as plt import numpy as np import os

plt.rcParams['font.family'] = 'sans-serif' plt.rcParams['font.sans-serif'] = 'Arial' plt.rc('font', size=14) plt.rcParams['pdf.fonttype'] = 42 input_dir = 'filtered_gene_bc_matrices/GRCh38/' counts_matrix = scipy.io.mmread(input_dir + '/matrix.mtx').T.tocsc() genes = np.array(scr.load_genes(input_dir + 'genes.tsv', delimiter='\t', column=1)) scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.06) doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2, min_cells=3,min_gene_variability_pctl=85, n_prin_comps=30)

Preprocessing... Simulating doublets... Embedding transcriptomes using PCA... Calculating doublet scores... Illegal instruction

zktuong commented 3 years ago

I also experienced this and managed to solve this by downgrading annoy to 1.16.3.