SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
Describe the bug
When running the run_scenicplus() step from the pbmc_multiome tutorial, during the "thresholding region to gene relationships" calculations, it proceeds as normal until after 10/14 where halfway it skips to initializing. It never finishes the 14 parts to completion. It does move on to the next steps and ultimately outputs a functional scplus_obj.pkl object. However, downstream I noticed my processed regulon dataset differed quite a bit from the tutorial. I was wondering if this apparent skipping of the last 3 of the 14 steps could possibly affect data processing?
Thanks in advance.
To Reproduce
from scenicplus.wrappers.run_scenicplus import run_scenicplus
try:
run_scenicplus(
scplus_obj = scplus_obj,
variable = ['GEX_celltype'],
species = 'hsapiens',
assembly = 'hg38',
tf_file = 'pbmc_tutorial/data/utoronto_human_tfs_v_1.01.txt',
save_path = os.path.join(work_dir, 'scenicplus'),
biomart_host = "http://sep2019.archive.ensembl.org/",
upstream = [1000, 150000],
downstream = [1000, 150000],
calculate_TF_eGRN_correlation = True,
calculate_DEGs_DARs = True,
export_to_loom_file = True,
export_to_UCSC_file = True,
path_bedToBigBed = 'pbmc_tutorial',
n_cpu = 12,
_temp_dir = os.path.join(tmp_dir, 'ray_spill'))
except Exception as e:
#in case of failure, still save the object
dill.dump(scplus_obj, open(os.path.join(work_dir, 'scenicplus/scplus_obj.pkl'), 'wb'), protocol=-1)
raise(e)
Error output
Processing: 0.95 quantile, positive r2g: 99%|██████████████████████████▋| 2067/2087 [00:39<00:00, 86.49it/s]
Processing: 0.95 quantile, positive r2g: 99%|██████████████████████████▊| 2076/2087 [00:39<00:00, 82.68it/s]
Processing: 0.95 quantile, positive r2g: 100%|██████████████████████████▉| 2085/2087 [00:39<00:00, 81.08it/s]
71%|███████████████████████████████████████████████████▍ | 10/14 [11:54<04:17, 64.43s/it]
Processing: Top 5 region-to-gene links per gene, positive r2g: 0%| | 0/2087 [00:00<?, ?it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 0%| | 5/2087 [00:00<00:42, 49.38it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 0%| | 10/2087 [00:00<00:48, 42.71it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 1%| | 15/2087 [00:00<00:55, 37.08it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 1%| | 19/2087 [00:00<01:07, 30.80it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 1%| | 23/2087 [00:00<01:08, 29.96it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 1%| | 27/2087 [00:00<01:16, 26.86it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 1%| | 31/2087 [00:00<01:11, 28.86it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 2%| | 35/2087 [00:01<01:15, 27.35it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 2%|▏ | 39/2087 [00:01<01:09, 29.41it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 2%|▏ | 43/2087 [00:01<01:11, 28.41it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 2%|▏ | 48/2087 [00:01<01:03, 31.94it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 2%|▏ | 52/2087 [00:01<01:02, 32.45it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 3%|▏ | 56/2087 [00:01<01:17, 26.22it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 3%|▏ | 61/2087 [00:02<01:09, 29.34it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 9%|▌ | 188/2087 [00:08<01:12, 26.14it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 9%|▌ | 197/2087 [00:08<00:58, 32.36it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 10%|▌ | 208/2087 [00:08<00:44, 41.86it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 10%|▋ | 218/2087 [00:08<00:50, 37.02it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 11%|▋ | 222/2087 [00:08<00:49, 37.56it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 11%|▋ | 227/2087 [00:08<00:47, 39.42it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 11%|▋ | 232/2087 [00:09<00:46, 40.27it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 11%|▋ | 237/2087 [00:09<00:45, 40.74it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 12%|▋ | 242/2087 [00:09<00:42, 43.07it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 12%|▋ | 247/2087 [00:09<00:45, 40.82it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 13%|▊ | 264/2087 [00:09<00:40, 44.54it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 14%|▊ | 286/2087 [00:10<00:50, 35.67it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 14%|▊ | 297/2087 [00:11<01:18, 22.71it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 15%|▊ | 303/2087 [00:11<01:03, 28.31it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 15%|▉ | 307/2087 [00:11<01:09, 25.57it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 15%|▉ | 310/2087 [00:11<01:19, 22.26it/s]
Processing: Top 5 region-to-gene links per gene, positive r2g: 15%|▉ | 313/2087 [00:11<01:25, 20.82it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 16%|▉ | 325/2087 [00:12<01:41, 17.44it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 16%|▉ | 337/2087 [00:12<01:03, 27.53it/s]
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Processing: Top 5 region-to-gene links per gene, positive r2g: 16%|▉ | 343/2087 [00:13<01:09, 25.24it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 21%|█ | 433/2087 [00:43<01:10, 23.42it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 21%|█ | 436/2087 [00:43<01:17, 21.38it/s]
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Processing: Top 15 region-to-gene links per gene, positive r2g: 22%|█ | 452/2087 [00:44<01:08, 23.72it/s]
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Processing: Top 15 region-to-gene links per gene, positive r2g: 22%|█ | 461/2087 [00:44<01:16, 21.32it/s]
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Processing: Top 15 region-to-gene links per gene, positive r2g: 23%|█▏ | 470/2087 [00:45<01:11, 22.53it/s]
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Processing: Top 15 region-to-gene links per gene, positive r2g: 23%|█▏ | 476/2087 [00:45<01:04, 25.08it/s]
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Processing: Top 15 region-to-gene links per gene, positive r2g: 24%|█▏ | 492/2087 [00:45<01:06, 23.95it/s]
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Processing: Top 15 region-to-gene links per gene, positive r2g: 30%|█▌ | 631/2087 [00:54<01:34, 15.44it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 30%|█▌ | 634/2087 [00:54<01:24, 17.22it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 30%|█▌ | 636/2087 [00:54<01:26, 16.79it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 31%|█▌ | 639/2087 [00:54<01:18, 18.54it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 31%|█▌ | 642/2087 [00:54<01:10, 20.54it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 31%|█▌ | 645/2087 [00:54<01:03, 22.67it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 31%|█▌ | 648/2087 [00:54<01:07, 21.47it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 31%|█▌ | 651/2087 [00:55<01:02, 23.07it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 31%|█▌ | 654/2087 [00:55<01:03, 22.61it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 31%|█▌ | 657/2087 [00:55<01:02, 22.72it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 32%|█▌ | 660/2087 [00:55<01:05, 21.75it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 32%|█▌ | 663/2087 [00:55<01:03, 22.54it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 32%|█▌ | 666/2087 [00:55<01:01, 23.07it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 32%|█▌ | 669/2087 [00:55<01:03, 22.40it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 32%|█▌ | 672/2087 [00:56<01:16, 18.61it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 32%|█▌ | 674/2087 [00:56<01:23, 16.98it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 32%|█▌ | 677/2087 [00:56<01:13, 19.06it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 33%|█▋ | 680/2087 [00:56<01:21, 17.21it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 33%|█▋ | 683/2087 [00:56<01:16, 18.38it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 33%|█▋ | 685/2087 [00:56<01:16, 18.33it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 33%|█▋ | 688/2087 [00:56<01:12, 19.37it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 33%|█▋ | 691/2087 [00:57<01:08, 20.48it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 33%|█▋ | 694/2087 [00:57<01:09, 19.91it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 33%|█▋ | 697/2087 [00:57<01:03, 21.84it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 34%|█▋ | 700/2087 [00:57<01:02, 22.09it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 34%|█▋ | 703/2087 [00:57<01:09, 19.92it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 34%|█▋ | 706/2087 [00:57<01:14, 18.50it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 34%|█▋ | 709/2087 [00:57<01:08, 20.22it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 34%|█▋ | 712/2087 [00:58<01:04, 21.17it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 34%|█▋ | 715/2087 [00:58<01:00, 22.71it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 34%|█▋ | 718/2087 [00:58<00:58, 23.52it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 35%|█▋ | 721/2087 [00:58<00:56, 24.21it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 35%|█▋ | 724/2087 [00:58<00:56, 24.09it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 35%|█▋ | 727/2087 [00:58<00:59, 22.96it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 35%|█▋ | 730/2087 [00:58<00:56, 24.01it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 35%|█▊ | 733/2087 [00:58<00:55, 24.48it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 35%|█▊ | 737/2087 [00:59<00:55, 24.51it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 35%|█▊ | 740/2087 [00:59<00:53, 25.20it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 36%|█▊ | 743/2087 [00:59<00:56, 23.95it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 36%|█▊ | 746/2087 [00:59<00:53, 25.01it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 36%|█▊ | 749/2087 [00:59<00:51, 25.85it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 36%|█▊ | 752/2087 [00:59<00:50, 26.67it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 36%|█▊ | 755/2087 [00:59<00:52, 25.24it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 36%|█▊ | 758/2087 [00:59<01:02, 21.31it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 36%|█▊ | 761/2087 [01:00<00:59, 22.41it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 37%|█▊ | 765/2087 [01:00<00:54, 24.08it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 37%|█▊ | 768/2087 [01:00<00:54, 24.13it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 37%|█▊ | 771/2087 [01:00<00:52, 25.28it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 37%|█▊ | 774/2087 [01:00<00:50, 25.89it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 37%|█▊ | 777/2087 [01:00<00:48, 26.84it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 37%|█▊ | 781/2087 [01:00<00:47, 27.65it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 38%|█▉ | 784/2087 [01:00<00:46, 28.01it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 38%|█▉ | 787/2087 [01:01<00:51, 25.06it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 38%|█▉ | 790/2087 [01:01<00:52, 24.84it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 38%|█▉ | 793/2087 [01:01<00:52, 24.64it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 38%|█▉ | 796/2087 [01:01<00:52, 24.74it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 38%|█▉ | 799/2087 [01:01<00:54, 23.75it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 38%|█▉ | 803/2087 [01:01<00:49, 25.92it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 39%|█▉ | 807/2087 [01:01<00:46, 27.40it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 39%|█▉ | 810/2087 [01:01<00:46, 27.33it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 39%|█▉ | 813/2087 [01:02<00:48, 26.31it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 39%|█▉ | 816/2087 [01:02<00:55, 22.82it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 39%|█▉ | 819/2087 [01:02<00:57, 21.97it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 39%|█▉ | 822/2087 [01:02<00:53, 23.55it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 40%|█▉ | 825/2087 [01:02<00:56, 22.33it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 40%|█▉ | 828/2087 [01:02<00:55, 22.87it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 40%|█▉ | 831/2087 [01:02<00:55, 22.52it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 40%|██ | 835/2087 [01:03<00:49, 25.24it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 40%|██ | 838/2087 [01:03<00:53, 23.50it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 40%|██ | 841/2087 [01:03<00:50, 24.75it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 40%|██ | 844/2087 [01:03<00:53, 23.28it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 41%|██ | 847/2087 [01:03<00:53, 23.29it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 41%|██ | 850/2087 [01:03<00:49, 24.90it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 41%|██ | 853/2087 [01:03<00:47, 26.03it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 41%|██ | 856/2087 [01:03<00:47, 25.69it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 41%|██ | 859/2087 [01:04<00:46, 26.55it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 41%|██ | 862/2087 [01:04<00:47, 25.86it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 41%|██ | 865/2087 [01:04<00:49, 24.86it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 42%|██ | 868/2087 [01:04<00:48, 25.22it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 42%|██ | 871/2087 [01:04<00:53, 22.89it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 42%|██ | 874/2087 [01:04<00:53, 22.55it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 42%|██ | 877/2087 [01:04<00:50, 24.05it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 42%|██ | 880/2087 [01:04<00:51, 23.58it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 42%|██ | 883/2087 [01:05<00:48, 24.86it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 42%|██ | 886/2087 [01:05<00:46, 25.78it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 43%|██▏ | 889/2087 [01:05<00:52, 22.92it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 43%|██▏ | 892/2087 [01:05<00:56, 21.25it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 43%|██▏ | 895/2087 [01:05<00:52, 22.67it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 43%|██▏ | 898/2087 [01:05<00:48, 24.38it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 43%|██▏ | 901/2087 [01:05<00:49, 24.01it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 43%|██▏ | 904/2087 [01:05<00:47, 24.82it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 43%|██▏ | 907/2087 [01:06<00:50, 23.26it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 44%|██▏ | 910/2087 [01:06<00:48, 24.37it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 44%|██▏ | 913/2087 [01:06<00:47, 24.48it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 44%|██▏ | 916/2087 [01:06<00:46, 25.46it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 44%|██▏ | 919/2087 [01:06<00:45, 25.59it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 44%|██▏ | 922/2087 [01:06<00:45, 25.50it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 44%|██▏ | 925/2087 [01:06<00:49, 23.25it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 44%|██▏ | 928/2087 [01:06<00:47, 24.42it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 45%|██▏ | 931/2087 [01:07<00:47, 24.55it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 45%|██▏ | 934/2087 [01:07<00:49, 23.43it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 45%|██▏ | 937/2087 [01:07<00:46, 24.85it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 45%|██▎ | 940/2087 [01:07<00:44, 25.49it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 45%|██▎ | 943/2087 [01:07<00:45, 25.21it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 45%|██▎ | 946/2087 [01:07<00:44, 25.76it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 45%|██▎ | 949/2087 [01:07<00:45, 24.81it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 46%|██▎ | 952/2087 [01:07<00:46, 24.50it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 46%|██▎ | 955/2087 [01:07<00:46, 24.53it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 46%|██▎ | 958/2087 [01:08<00:45, 24.62it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 46%|██▎ | 961/2087 [01:08<00:45, 24.97it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 46%|██▎ | 964/2087 [01:08<00:43, 25.67it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 46%|██▎ | 967/2087 [01:08<00:41, 26.81it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 46%|██▎ | 970/2087 [01:08<00:42, 26.17it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 47%|██▎ | 973/2087 [01:08<00:41, 26.81it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 47%|██▎ | 976/2087 [01:08<00:41, 26.83it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 47%|██▎ | 979/2087 [01:08<00:46, 23.75it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 47%|██▎ | 982/2087 [01:09<00:45, 24.07it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 47%|██▎ | 985/2087 [01:09<00:47, 23.05it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 47%|██▎ | 988/2087 [01:09<00:49, 22.23it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 47%|██▎ | 991/2087 [01:09<00:51, 21.45it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 48%|██▍ | 994/2087 [01:09<00:53, 20.44it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 48%|██▍ | 997/2087 [01:09<00:49, 22.00it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 48%|█▉ | 1000/2087 [01:09<00:48, 22.61it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 48%|█▉ | 1003/2087 [01:10<00:54, 19.93it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 48%|█▉ | 1006/2087 [01:10<00:51, 20.99it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 48%|█▉ | 1009/2087 [01:10<00:49, 21.86it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 48%|█▉ | 1012/2087 [01:10<00:56, 19.09it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 49%|█▉ | 1015/2087 [01:10<01:07, 15.84it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 49%|█▉ | 1017/2087 [01:10<01:10, 15.27it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 49%|█▉ | 1019/2087 [01:11<01:12, 14.73it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 49%|█▉ | 1021/2087 [01:11<01:10, 15.07it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 49%|█▉ | 1024/2087 [01:11<01:03, 16.71it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 49%|█▉ | 1026/2087 [01:11<01:04, 16.36it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 49%|█▉ | 1028/2087 [01:11<01:12, 14.70it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 49%|█▉ | 1031/2087 [01:11<01:03, 16.74it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 50%|█▉ | 1034/2087 [01:11<00:57, 18.19it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 50%|█▉ | 1036/2087 [01:12<01:06, 15.84it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 50%|█▉ | 1039/2087 [01:12<01:01, 16.99it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 50%|█▉ | 1042/2087 [01:12<00:58, 17.86it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 50%|██ | 1044/2087 [01:12<00:59, 17.60it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 50%|██ | 1047/2087 [01:12<00:55, 18.84it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 50%|██ | 1049/2087 [01:12<00:56, 18.38it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 50%|██ | 1052/2087 [01:12<00:49, 20.82it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 51%|██ | 1055/2087 [01:13<00:49, 20.70it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 51%|██ | 1058/2087 [01:13<00:46, 22.23it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 51%|██ | 1061/2087 [01:13<00:53, 19.19it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 51%|██ | 1064/2087 [01:13<01:03, 16.23it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 51%|██ | 1067/2087 [01:13<00:56, 18.00it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 51%|██ | 1069/2087 [01:13<00:58, 17.35it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 51%|██ | 1071/2087 [01:13<00:58, 17.46it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 51%|██ | 1073/2087 [01:14<00:56, 17.99it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 52%|██ | 1075/2087 [01:14<00:55, 18.25it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 52%|██ | 1078/2087 [01:14<00:52, 19.17it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 52%|██ | 1081/2087 [01:14<00:49, 20.14it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 52%|██ | 1084/2087 [01:14<00:46, 21.47it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 52%|██ | 1087/2087 [01:14<00:47, 21.16it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 52%|██ | 1090/2087 [01:14<00:43, 22.75it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 52%|██ | 1093/2087 [01:15<00:48, 20.41it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 53%|██ | 1096/2087 [01:15<00:47, 20.70it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 53%|██ | 1099/2087 [01:15<00:50, 19.67it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 53%|██ | 1102/2087 [01:15<00:49, 20.01it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 53%|██ | 1105/2087 [01:15<00:44, 21.85it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 53%|██ | 1108/2087 [01:15<00:41, 23.40it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 53%|██▏ | 1111/2087 [01:16<00:59, 16.29it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 53%|██▏ | 1113/2087 [01:16<01:04, 15.12it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 53%|██▏ | 1115/2087 [01:16<01:05, 14.76it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 54%|██▏ | 1117/2087 [01:16<01:06, 14.69it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 54%|██▏ | 1119/2087 [01:16<01:02, 15.38it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 54%|██▏ | 1122/2087 [01:16<00:54, 17.73it/s]
Processing: Top 15 region-to-gene links per gene, positive r2g: 54%|██▏ | 1124/2087 [01:16<01:09, 13.79it/s]
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(_ray_run_gsea_for_e_module pid=32228) /root/miniconda3/envs/SCENICplus/lib/python3.8/site-packages/gseapy/algorithm.py:71: RuntimeWarning: divide by zero encountered in divide
(_ray_run_gsea_for_e_module pid=32228) norm_tag = 1.0/sum_correl_tag
(_ray_run_gsea_for_e_module pid=32228) /root/miniconda3/envs/SCENICplus/lib/python3.8/site-packages/gseapy/algorithm.py:74: RuntimeWarning: invalid value encountered in multiply
(_ray_run_gsea_for_e_module pid=32228) RES = np.cumsum(tag_indicator * correl_vector * norm_tag - no_tag_indicator * norm_no_tag, axis=axis)
2024-02-20 11:54:59,303 GSEA INFO Subsetting on adjusted pvalue: 1, minimal NES: 0 and minimal leading edge genes 10
2024-02-20 11:55:00,772 GSEA INFO Merging eRegulons
2024-02-20 11:55:01,165 GSEA INFO Storing eRegulons in .uns[eRegulons].
2024-02-20 11:55:20,057 SCENIC+_wrapper INFO Formatting eGRNs
2024-02-20 11:57:21,678 SCENIC+_wrapper INFO Converting eGRNs to signatures
2024-02-20 11:57:25,318 SCENIC+_wrapper INFO Calculating eGRNs AUC
2024-02-20 11:57:25,319 SCENIC+_wrapper INFO Calculating region ranking
2024-02-20 11:58:34,507 SCENIC+_wrapper INFO Calculating eGRNs region based AUC
2024-02-20 11:58:51,238 SCENIC+_wrapper INFO Calculating gene ranking
2024-02-20 11:58:56,773 SCENIC+_wrapper INFO Calculating eGRNs gene based AUC
2024-02-20 11:59:04,085 SCENIC+_wrapper INFO Calculating TF-eGRNs AUC correlation
2024-02-20 11:59:17,634 SCENIC+_wrapper INFO Binarizing eGRNs AUC
2024-02-20 12:02:34,405 SCENIC+_wrapper INFO Making eGRNs AUC UMAP
2024-02-20 12:02:45,072 SCENIC+_wrapper INFO Making eGRNs AUC tSNE
2024-02-20 12:02:50,975 SCENIC+_wrapper INFO Calculating eRSS
2024-02-20 12:02:53,878 SCENIC+_wrapper INFO Calculating DEGs/DARs
2024-02-20 12:02:53,879 SCENIC+ INFO Calculating DEGs for variable GEX_celltype
2024-02-20 12:02:54,714 SCENIC+ INFO There are 4760 variable features
... storing 'ACC_celltype' as categorical
... storing 'ACC_sample_id' as categorical
2024-02-20 12:02:56,812 SCENIC+ INFO Finished calculating DEGs for variable GEX_celltype
2024-02-20 12:02:56,814 SCENIC+ INFO Calculating DARs for variable GEX_celltype
2024-02-20 12:03:08,980 SCENIC+ INFO There are 54447 variable features
... storing 'ACC_celltype' as categorical
... storing 'ACC_sample_id' as categorical
2024-02-20 12:03:37,015 SCENIC+ INFO Finished calculating DARs for variable GEX_celltype
2024-02-20 12:03:37,017 SCENIC+_wrapper INFO Exporting to loom file
2024-02-20 12:03:37,019 SCENIC+ INFO Formatting data
2024-02-20 12:03:39,281 SCENIC+ INFO Creating minimal loom
2024-02-20 12:03:42,772 SCENIC+ INFO Adding annotations
2024-02-20 12:03:43,707 SCENIC+ INFO Adding clusterings
2024-02-20 12:03:43,729 SCENIC+ INFO Adding markers
2024-02-20 12:03:43,963 SCENIC+ INFO Exporting
2024-02-20 12:03:47,033 SCENIC+ INFO Formatting data
2024-02-20 12:04:01,489 SCENIC+ INFO Creating minimal loom
2024-02-20 12:04:50,580 SCENIC+ INFO Adding annotations
2024-02-20 12:05:00,404 SCENIC+ INFO Adding clusterings
2024-02-20 12:05:00,451 SCENIC+ INFO Adding markers
2024-02-20 12:05:02,870 SCENIC+ INFO Exporting
2024-02-20 12:05:29,671 SCENIC+_wrapper INFO Exporting to UCSC
2024-02-20 12:05:30,294 R2G INFO Downloading gene annotation from biomart, using dataset: hsapiens_gene_ensembl
2024-02-20 12:05:30,668 R2G INFO Formatting data ...
2024-02-20 12:05:48,537 R2G INFO Writing data to: pbmc_tutorial/scenicplus/r2g.rho.bed
2024-02-20 12:05:49,274 R2G INFO Writing data to: pbmc_tutorial/scenicplus/r2g.rho.bb
2024-02-20 12:05:52,048 R2G INFO Downloading gene annotation from biomart, using dataset: hsapiens_gene_ensembl
2024-02-20 12:05:52,483 R2G INFO Formatting data ...
2024-02-20 12:06:10,860 R2G INFO Writing data to: pbmc_tutorial/scenicplus/r2g.importance.bed
2024-02-20 12:06:11,605 R2G INFO Writing data to: pbmc_tutorial/scenicplus/r2g.importance.bb
2024-02-20 12:06:14,884 SCENIC+_wrapper INFO Saving object
2024-02-20 12:17:34,861 SCENIC+_wrapper INFO Finished! Took 128.90375864903132 minutes
Expected behavior
Have the Thresholding region to gene relationships step of run_scenicplus() complete all 14 parts.
Version (please complete the following information):
Python: Python 3.8.18
SCENIC+: 1.0.1.dev6+ge5ba6fc
Additional context
In downstream steps, some eRegulons appear to be missing from my dataset after running run_scenicplus(). For example, during the step "dotplot heatmap", I have noticeably less eRegulons displayed, and subsequently less eRegulons kept (41) compared to the tutorial (76).
Describe the bug When running the run_scenicplus() step from the pbmc_multiome tutorial, during the "thresholding region to gene relationships" calculations, it proceeds as normal until after 10/14 where halfway it skips to initializing. It never finishes the 14 parts to completion. It does move on to the next steps and ultimately outputs a functional scplus_obj.pkl object. However, downstream I noticed my processed regulon dataset differed quite a bit from the tutorial. I was wondering if this apparent skipping of the last 3 of the 14 steps could possibly affect data processing?
Thanks in advance.
To Reproduce
Error output
Expected behavior Have the Thresholding region to gene relationships step of run_scenicplus() complete all 14 parts.
Version (please complete the following information):
Additional context In downstream steps, some eRegulons appear to be missing from my dataset after running run_scenicplus(). For example, during the step "dotplot heatmap", I have noticeably less eRegulons displayed, and subsequently less eRegulons kept (41) compared to the tutorial (76).
Screenshots
My dotplot heatmap:
Tutorial's dotplot heatmap: