cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1713-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/1713-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 7596 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 8259cad76a)
cellbender:remove-background: 2024-06-06 14:54:30
cellbender:remove-background: Running remove-background
cellbender:remove-background: Loading data from /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1713-Bipolar-DLPFC.raw_feature_bc_matrix.h5
cellbender:remove-background: CellRanger v3 format
cellbender:remove-background: Features in dataset: 36601 Gene Expression
cellbender:remove-background: Trimming features for inference.
cellbender:remove-background: 30838 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 724
cellbender:remove-background: Prior on counts for empty droplets is 43
cellbender:remove-background: Excluding 7270 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 23568 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 21
cellbender:remove-background: Using 7596 probable cell barcodes, plus an additional 12404 barcodes, and 46710 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 43 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpuf74pbrc
cellbender:remove-background: No saved checkpoint.
cellbender:remove-background: No checkpoint loaded.
cellbender:remove-background: Running inference...
cellbender:remove-background: [epoch 001]  average training loss: 2442.0807
cellbender:remove-background: [epoch 002]  average training loss: 2006.0542  (6.9 seconds per epoch)
cellbender:remove-background: Will checkpoint every 61 epochs
cellbender:remove-background: [epoch 003]  average training loss: 1806.3831
cellbender:remove-background: [epoch 004]  average training loss: 1671.9851
cellbender:remove-background: [epoch 005]  average training loss: 1635.9102
cellbender:remove-background: [epoch 005] average test loss: 1726.7569
cellbender:remove-background: [epoch 006]  average training loss: 1618.5542
cellbender:remove-background: [epoch 007]  average training loss: 1597.8788
cellbender:remove-background: [epoch 008]  average training loss: 1582.6984
cellbender:remove-background: [epoch 009]  average training loss: 1588.0055
cellbender:remove-background: [epoch 010]  average training loss: 1571.3508
cellbender:remove-background: [epoch 010] average test loss: 1613.1150
cellbender:remove-background: [epoch 011]  average training loss: 1573.0881
cellbender:remove-background: [epoch 012]  average training loss: 1562.4250
cellbender:remove-background: [epoch 013]  average training loss: 1520.7079
cellbender:remove-background: [epoch 014]  average training loss: 1507.2326
cellbender:remove-background: [epoch 015]  average training loss: 1494.1469
cellbender:remove-background: [epoch 015] average test loss: 1533.6516
cellbender:remove-background: [epoch 016]  average training loss: 1488.8424
cellbender:remove-background: [epoch 017]  average training loss: 1488.5398
cellbender:remove-background: [epoch 018]  average training loss: 1480.7262
cellbender:remove-background: [epoch 019]  average training loss: 1472.9263
cellbender:remove-background: [epoch 020]  average training loss: 1464.8648
cellbender:remove-background: [epoch 020] average test loss: 1516.0002
cellbender:remove-background: [epoch 021]  average training loss: 1466.8859
cellbender:remove-background: [epoch 022]  average training loss: 1466.4776
cellbender:remove-background: [epoch 023]  average training loss: 1464.5436
cellbender:remove-background: [epoch 024]  average training loss: 1462.4824
cellbender:remove-background: [epoch 025]  average training loss: 1460.7349
cellbender:remove-background: [epoch 025] average test loss: 1504.6869
cellbender:remove-background: [epoch 026]  average training loss: 1454.8291
cellbender:remove-background: [epoch 027]  average training loss: 1443.5107
cellbender:remove-background: [epoch 028]  average training loss: 1431.4090
cellbender:remove-background: [epoch 029]  average training loss: 1424.3520
cellbender:remove-background: [epoch 030]  average training loss: 1419.7152
cellbender:remove-background: [epoch 030] average test loss: 1464.1415
cellbender:remove-background: [epoch 031]  average training loss: 1415.2144
cellbender:remove-background: [epoch 032]  average training loss: 1412.9258
cellbender:remove-background: [epoch 033]  average training loss: 1411.7483
cellbender:remove-background: [epoch 034]  average training loss: 1409.3940
cellbender:remove-background: [epoch 035]  average training loss: 1408.2092
cellbender:remove-background: [epoch 035] average test loss: 1447.6288
cellbender:remove-background: [epoch 036]  average training loss: 1406.4331
cellbender:remove-background: [epoch 037]  average training loss: 1406.0850
cellbender:remove-background: [epoch 038]  average training loss: 1403.9355
cellbender:remove-background: [epoch 039]  average training loss: 1403.1096
cellbender:remove-background: [epoch 040]  average training loss: 1400.7498
cellbender:remove-background: [epoch 040] average test loss: 1440.7462
cellbender:remove-background: [epoch 041]  average training loss: 1400.6987
cellbender:remove-background: [epoch 042]  average training loss: 1398.4208
cellbender:remove-background: [epoch 043]  average training loss: 1398.7759
cellbender:remove-background: [epoch 044]  average training loss: 1396.2474
cellbender:remove-background: [epoch 045]  average training loss: 1394.8106
cellbender:remove-background: [epoch 045] average test loss: 1433.3025
cellbender:remove-background: [epoch 046]  average training loss: 1393.8498
cellbender:remove-background: [epoch 047]  average training loss: 1393.4555
cellbender:remove-background: [epoch 048]  average training loss: 1391.8148
cellbender:remove-background: [epoch 049]  average training loss: 1391.6531
cellbender:remove-background: [epoch 050]  average training loss: 1391.2909
cellbender:remove-background: [epoch 050] average test loss: 1431.3592
cellbender:remove-background: [epoch 051]  average training loss: 1388.9401
cellbender:remove-background: [epoch 052]  average training loss: 1388.6147
cellbender:remove-background: [epoch 053]  average training loss: 1388.8606
cellbender:remove-background: [epoch 054]  average training loss: 1387.0142
cellbender:remove-background: [epoch 055]  average training loss: 1388.0299
cellbender:remove-background: [epoch 055] average test loss: 1434.0066
cellbender:remove-background: [epoch 056]  average training loss: 1387.6915
cellbender:remove-background: [epoch 057]  average training loss: 1386.3920
cellbender:remove-background: [epoch 058]  average training loss: 1383.9435
cellbender:remove-background: [epoch 059]  average training loss: 1383.0074
cellbender:remove-background: [epoch 060]  average training loss: 1385.8450
cellbender:remove-background: [epoch 060] average test loss: 1431.0855
cellbender:remove-background: [epoch 061]  average training loss: 1383.6468
cellbender:remove-background: Saving a checkpoint...
cellbender:remove-background: Saved checkpoint as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 062]  average training loss: 1385.4831
cellbender:remove-background: [epoch 063]  average training loss: 1382.0376
cellbender:remove-background: [epoch 064]  average training loss: 1383.5899
cellbender:remove-background: [epoch 065]  average training loss: 1381.1688
cellbender:remove-background: [epoch 065] average test loss: 1434.7130
cellbender:remove-background: [epoch 066]  average training loss: 1382.4166
cellbender:remove-background: [epoch 067]  average training loss: 1384.9126
cellbender:remove-background: [epoch 068]  average training loss: 1379.3897
cellbender:remove-background: [epoch 069]  average training loss: 1380.4485
cellbender:remove-background: [epoch 070]  average training loss: 1378.9310
cellbender:remove-background: [epoch 070] average test loss: 1422.8469
cellbender:remove-background: [epoch 071]  average training loss: 1381.8126
cellbender:remove-background: [epoch 072]  average training loss: 1383.7688
cellbender:remove-background: [epoch 073]  average training loss: 1379.5736
cellbender:remove-background: [epoch 074]  average training loss: 1376.2985
cellbender:remove-background: [epoch 075]  average training loss: 1379.2348
cellbender:remove-background: [epoch 075] average test loss: 1435.2666
cellbender:remove-background: [epoch 076]  average training loss: 1373.9446
cellbender:remove-background: [epoch 077]  average training loss: 1378.9822
cellbender:remove-background: [epoch 078]  average training loss: 1377.2008
cellbender:remove-background: [epoch 079]  average training loss: 1378.9750
cellbender:remove-background: [epoch 080]  average training loss: 1379.6933
cellbender:remove-background: [epoch 080] average test loss: 1447.0518
cellbender:remove-background: [epoch 081]  average training loss: 1379.8120
cellbender:remove-background: [epoch 082]  average training loss: 1378.0165
cellbender:remove-background: [epoch 083]  average training loss: 1378.2152
cellbender:remove-background: [epoch 084]  average training loss: 1382.8066
cellbender:remove-background: [epoch 085]  average training loss: 1378.5929
cellbender:remove-background: [epoch 085] average test loss: 1425.0529
cellbender:remove-background: [epoch 086]  average training loss: 1377.0223
cellbender:remove-background: [epoch 087]  average training loss: 1378.8806
cellbender:remove-background: [epoch 088]  average training loss: 1377.1368
cellbender:remove-background: [epoch 089]  average training loss: 1379.6332
cellbender:remove-background: [epoch 090]  average training loss: 1376.2499
cellbender:remove-background: [epoch 090] average test loss: 1428.5290
cellbender:remove-background: [epoch 091]  average training loss: 1377.9011
cellbender:remove-background: [epoch 092]  average training loss: 1377.8384
cellbender:remove-background: [epoch 093]  average training loss: 1375.5543
cellbender:remove-background: [epoch 094]  average training loss: 1373.2188
cellbender:remove-background: [epoch 095]  average training loss: 1375.9446
cellbender:remove-background: [epoch 095] average test loss: 1446.5147
cellbender:remove-background: [epoch 096]  average training loss: 1376.8646
cellbender:remove-background: [epoch 097]  average training loss: 1375.4439
cellbender:remove-background: [epoch 098]  average training loss: 1371.8820
cellbender:remove-background: [epoch 099]  average training loss: 1372.6769
cellbender:remove-background: [epoch 100]  average training loss: 1372.0413
cellbender:remove-background: [epoch 100] average test loss: 1434.7669
cellbender:remove-background: [epoch 101]  average training loss: 1371.8074
cellbender:remove-background: [epoch 102]  average training loss: 1369.3880
cellbender:remove-background: [epoch 103]  average training loss: 1368.2412
cellbender:remove-background: [epoch 104]  average training loss: 1369.3335
cellbender:remove-background: [epoch 105]  average training loss: 1371.9212
cellbender:remove-background: [epoch 105] average test loss: 1426.3132
cellbender:remove-background: [epoch 106]  average training loss: 1370.7091
cellbender:remove-background: [epoch 107]  average training loss: 1370.0114
cellbender:remove-background: [epoch 108]  average training loss: 1367.2433
cellbender:remove-background: [epoch 109]  average training loss: 1367.6488
cellbender:remove-background: [epoch 110]  average training loss: 1368.9511
cellbender:remove-background: [epoch 110] average test loss: 1430.8750
cellbender:remove-background: [epoch 111]  average training loss: 1371.5114
cellbender:remove-background: [epoch 112]  average training loss: 1370.7413
cellbender:remove-background: [epoch 113]  average training loss: 1370.3375
cellbender:remove-background: [epoch 114]  average training loss: 1370.1731
cellbender:remove-background: [epoch 115]  average training loss: 1369.9065
cellbender:remove-background: [epoch 115] average test loss: 1433.2720
cellbender:remove-background: [epoch 116]  average training loss: 1372.9656
cellbender:remove-background: [epoch 117]  average training loss: 1368.4539
cellbender:remove-background: [epoch 118]  average training loss: 1370.8705
cellbender:remove-background: [epoch 119]  average training loss: 1367.5612
cellbender:remove-background: [epoch 120]  average training loss: 1367.8521
cellbender:remove-background: [epoch 120] average test loss: 1427.7255
cellbender:remove-background: [epoch 121]  average training loss: 1366.0971
cellbender:remove-background: [epoch 122]  average training loss: 1368.4571
cellbender:remove-background: Saving a checkpoint...
cellbender:remove-background: Saved checkpoint as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 123]  average training loss: 1367.3091
cellbender:remove-background: [epoch 124]  average training loss: 1368.5787
cellbender:remove-background: [epoch 125]  average training loss: 1367.3289
cellbender:remove-background: [epoch 125] average test loss: 1436.5918
cellbender:remove-background: [epoch 126]  average training loss: 1366.1604
cellbender:remove-background: [epoch 127]  average training loss: 1368.7978
cellbender:remove-background: [epoch 128]  average training loss: 1367.8397
cellbender:remove-background: [epoch 129]  average training loss: 1367.3237
cellbender:remove-background: [epoch 130]  average training loss: 1368.4662
cellbender:remove-background: [epoch 130] average test loss: 1435.2861
cellbender:remove-background: [epoch 131]  average training loss: 1366.9738
cellbender:remove-background: [epoch 132]  average training loss: 1366.3769
cellbender:remove-background: [epoch 133]  average training loss: 1367.3579
cellbender:remove-background: [epoch 134]  average training loss: 1366.9170
cellbender:remove-background: [epoch 135]  average training loss: 1369.2439
cellbender:remove-background: [epoch 135] average test loss: 1440.5974
cellbender:remove-background: [epoch 136]  average training loss: 1366.0891
cellbender:remove-background: [epoch 137]  average training loss: 1366.2867
cellbender:remove-background: [epoch 138]  average training loss: 1366.3091
cellbender:remove-background: [epoch 139]  average training loss: 1367.6877
cellbender:remove-background: [epoch 140]  average training loss: 1368.0100
cellbender:remove-background: [epoch 140] average test loss: 1438.8026
cellbender:remove-background: [epoch 141]  average training loss: 1368.2348
cellbender:remove-background: [epoch 142]  average training loss: 1366.1531
cellbender:remove-background: [epoch 143]  average training loss: 1367.9368
cellbender:remove-background: [epoch 144]  average training loss: 1367.2624
cellbender:remove-background: [epoch 145]  average training loss: 1366.8751
cellbender:remove-background: [epoch 145] average test loss: 1435.6090
cellbender:remove-background: [epoch 146]  average training loss: 1365.8794
cellbender:remove-background: [epoch 147]  average training loss: 1366.6386
cellbender:remove-background: [epoch 148]  average training loss: 1365.4515
cellbender:remove-background: [epoch 149]  average training loss: 1367.0052
cellbender:remove-background: [epoch 150]  average training loss: 1367.5483
cellbender:remove-background: [epoch 150] average test loss: 1430.7714
cellbender:remove-background: Saving a checkpoint...
cellbender:remove-background: Saved checkpoint as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:14:36
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp25s11j0z
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp25s11j0z
/tmp/tmp25s11j0z/8259cad76a_random.pyro
/tmp/tmp25s11j0z/8259cad76a_random.cuda
/tmp/tmp25s11j0z/8259cad76a_model.torch
/tmp/tmp25s11j0z/8259cad76a_optim.torch
/tmp/tmp25s11j0z/8259cad76a_optim.pyro
/tmp/tmp25s11j0z/8259cad76a_params.pyro
/tmp/tmp25s11j0z/8259cad76a_train.loaderstate
/tmp/tmp25s11j0z/8259cad76a_test.loaderstate
/tmp/tmp25s11j0z/8259cad76a_args.npy
cellbender:remove-background: Posterior not currently included in checkpoint.
cellbender:remove-background: Computing posterior noise count probabilities in mini-batches.
cellbender:remove-background: Working on chunk (1/55)
cellbender:remove-background:     [0.04 mins per chunk]
cellbender:remove-background: Working on chunk (2/55)
cellbender:remove-background: Working on chunk (3/55)
cellbender:remove-background: Working on chunk (4/55)
cellbender:remove-background: Working on chunk (5/55)
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cellbender:remove-background: Working on chunk (17/55)
cellbender:remove-background: Working on chunk (18/55)
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cellbender:remove-background: Working on chunk (20/55)
cellbender:remove-background: Working on chunk (21/55)
cellbender:remove-background: Working on chunk (22/55)
cellbender:remove-background: Working on chunk (23/55)
cellbender:remove-background: Working on chunk (24/55)
cellbender:remove-background: Working on chunk (25/55)
cellbender:remove-background: Working on chunk (26/55)
cellbender:remove-background: Working on chunk (27/55)
cellbender:remove-background: Working on chunk (28/55)
cellbender:remove-background: Working on chunk (29/55)
cellbender:remove-background: Working on chunk (30/55)
cellbender:remove-background: Working on chunk (31/55)
cellbender:remove-background: Working on chunk (32/55)
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cellbender:remove-background: Working on chunk (34/55)
cellbender:remove-background: Working on chunk (35/55)
cellbender:remove-background: Working on chunk (36/55)
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cellbender:remove-background: Working on chunk (38/55)
cellbender:remove-background: Working on chunk (39/55)
cellbender:remove-background: Working on chunk (40/55)
cellbender:remove-background: Working on chunk (41/55)
cellbender:remove-background: Working on chunk (42/55)
cellbender:remove-background: Working on chunk (43/55)
cellbender:remove-background: Working on chunk (44/55)
cellbender:remove-background: Working on chunk (45/55)
cellbender:remove-background: Working on chunk (46/55)
cellbender:remove-background: Working on chunk (47/55)
cellbender:remove-background: Working on chunk (48/55)
cellbender:remove-background: Working on chunk (49/55)
cellbender:remove-background: Working on chunk (50/55)
cellbender:remove-background: Working on chunk (51/55)
cellbender:remove-background: Working on chunk (52/55)
cellbender:remove-background: Working on chunk (53/55)
cellbender:remove-background: Working on chunk (54/55)
cellbender:remove-background: Working on chunk (55/55)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/1713-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/1713-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:18:07

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/1713-Bipolar-DLPFC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/1713-Bipolar-DLPFC.cellbender.output_cell_barcodes.csv
cellbender:remove-background: Computing target noise counts per gene for MCKP estimator
cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01
cellbender:remove-background: Computing denoised counts using mckp estimator
cellbender:remove-background: Working on chunk (1/7)
cellbender:remove-background:     [0.54 mins per chunk]
cellbender:remove-background: Working on chunk (2/7)
cellbender:remove-background: Working on chunk (3/7)
cellbender:remove-background: Working on chunk (4/7)
cellbender:remove-background: Working on chunk (5/7)
cellbender:remove-background: Working on chunk (6/7)
cellbender:remove-background: Working on chunk (7/7)
cellbender:remove-background: 2024-06-06 15:22:04 Total MCKP estimation time = 225.96 sec
cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/1713-Bipolar-DLPFC.cellbender.output.h5
cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/1713-Bipolar-DLPFC.cellbender.output_filtered.h5
cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/1713-Bipolar-DLPFC.cellbender.output_metrics.csv
Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    from lxml.html.clean import clean_html
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in <module>
    ) from None
ImportError: lxml.html.clean module is now a separate project lxml_html_clean.
Install lxml[html_clean] or lxml_html_clean directly.
Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    from lxml.html.clean import clean_html
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in <module>
    ) from None
ImportError: lxml.html.clean module is now a separate project lxml_html_clean.
Install lxml[html_clean] or lxml_html_clean directly.
mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory
rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory
cellbender:remove-background: Unable to create report.
cellbender:remove-background: Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics
    output=html_report_file,
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html
    title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')),
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html
    with open(file, mode='r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1713-Bipolar-DLPFC/1713-Bipolar-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:22:13