cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1734-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1734-Bipolar-dACC/1734-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 6599 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash a0031998c5)
cellbender:remove-background: 2024-06-06 14:52:11
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/1734-Bipolar-dACC.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: 30587 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 591
cellbender:remove-background: Prior on counts for empty droplets is 47
cellbender:remove-background: Excluding 9406 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 21181 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 23
cellbender:remove-background: Using 6599 probable cell barcodes, plus an additional 13401 barcodes, and 54698 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 47 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpld9wz87r
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: 2024.6899
cellbender:remove-background: [epoch 002]  average training loss: 1688.6325  (5.9 seconds per epoch)
cellbender:remove-background: Will checkpoint every 72 epochs
cellbender:remove-background: [epoch 003]  average training loss: 1507.8102
cellbender:remove-background: [epoch 004]  average training loss: 1390.6414
cellbender:remove-background: [epoch 005]  average training loss: 1346.8613
cellbender:remove-background: [epoch 005] average test loss: 1474.2457
cellbender:remove-background: [epoch 006]  average training loss: 1334.8096
cellbender:remove-background: [epoch 007]  average training loss: 1315.5255
cellbender:remove-background: [epoch 008]  average training loss: 1308.4342
cellbender:remove-background: [epoch 009]  average training loss: 1304.2771
cellbender:remove-background: [epoch 010]  average training loss: 1292.1275
cellbender:remove-background: [epoch 010] average test loss: 1338.1342
cellbender:remove-background: [epoch 011]  average training loss: 1301.5026
cellbender:remove-background: [epoch 012]  average training loss: 1298.5004
cellbender:remove-background: [epoch 013]  average training loss: 1286.0620
cellbender:remove-background: [epoch 014]  average training loss: 1272.1815
cellbender:remove-background: [epoch 015]  average training loss: 1221.2447
cellbender:remove-background: [epoch 015] average test loss: 1274.1493
cellbender:remove-background: [epoch 016]  average training loss: 1217.5707
cellbender:remove-background: [epoch 017]  average training loss: 1218.2456
cellbender:remove-background: [epoch 018]  average training loss: 1212.2575
cellbender:remove-background: [epoch 019]  average training loss: 1208.2867
cellbender:remove-background: [epoch 020]  average training loss: 1202.0232
cellbender:remove-background: [epoch 020] average test loss: 1261.4844
cellbender:remove-background: [epoch 021]  average training loss: 1201.7601
cellbender:remove-background: [epoch 022]  average training loss: 1200.7586
cellbender:remove-background: [epoch 023]  average training loss: 1198.8021
cellbender:remove-background: [epoch 024]  average training loss: 1196.8784
cellbender:remove-background: [epoch 025]  average training loss: 1196.2063
cellbender:remove-background: [epoch 025] average test loss: 1243.1262
cellbender:remove-background: [epoch 026]  average training loss: 1194.4594
cellbender:remove-background: [epoch 027]  average training loss: 1193.1461
cellbender:remove-background: [epoch 028]  average training loss: 1191.6388
cellbender:remove-background: [epoch 029]  average training loss: 1190.4620
cellbender:remove-background: [epoch 030]  average training loss: 1187.9729
cellbender:remove-background: [epoch 030] average test loss: 1229.4547
cellbender:remove-background: [epoch 031]  average training loss: 1185.3941
cellbender:remove-background: [epoch 032]  average training loss: 1180.9074
cellbender:remove-background: [epoch 033]  average training loss: 1178.5799
cellbender:remove-background: [epoch 034]  average training loss: 1175.8250
cellbender:remove-background: [epoch 035]  average training loss: 1173.6498
cellbender:remove-background: [epoch 035] average test loss: 1228.4851
cellbender:remove-background: [epoch 036]  average training loss: 1173.7098
cellbender:remove-background: [epoch 037]  average training loss: 1171.7027
cellbender:remove-background: [epoch 038]  average training loss: 1170.5857
cellbender:remove-background: [epoch 039]  average training loss: 1168.7070
cellbender:remove-background: [epoch 040]  average training loss: 1167.4466
cellbender:remove-background: [epoch 040] average test loss: 1214.1122
cellbender:remove-background: [epoch 041]  average training loss: 1168.3475
cellbender:remove-background: [epoch 042]  average training loss: 1166.1070
cellbender:remove-background: [epoch 043]  average training loss: 1166.2227
cellbender:remove-background: [epoch 044]  average training loss: 1165.1221
cellbender:remove-background: [epoch 045]  average training loss: 1164.8919
cellbender:remove-background: [epoch 045] average test loss: 1216.6847
cellbender:remove-background: [epoch 046]  average training loss: 1164.8789
cellbender:remove-background: [epoch 047]  average training loss: 1163.7790
cellbender:remove-background: [epoch 048]  average training loss: 1162.2861
cellbender:remove-background: [epoch 049]  average training loss: 1162.2388
cellbender:remove-background: [epoch 050]  average training loss: 1162.5288
cellbender:remove-background: [epoch 050] average test loss: 1204.0237
cellbender:remove-background: [epoch 051]  average training loss: 1158.9716
cellbender:remove-background: [epoch 052]  average training loss: 1161.0301
cellbender:remove-background: [epoch 053]  average training loss: 1158.4831
cellbender:remove-background: [epoch 054]  average training loss: 1159.4786
cellbender:remove-background: [epoch 055]  average training loss: 1157.7945
cellbender:remove-background: [epoch 055] average test loss: 1205.4855
cellbender:remove-background: [epoch 056]  average training loss: 1157.6245
cellbender:remove-background: [epoch 057]  average training loss: 1158.9173
cellbender:remove-background: [epoch 058]  average training loss: 1158.0921
cellbender:remove-background: [epoch 059]  average training loss: 1160.5707
cellbender:remove-background: [epoch 060]  average training loss: 1155.2516
cellbender:remove-background: [epoch 060] average test loss: 1209.7896
cellbender:remove-background: [epoch 061]  average training loss: 1159.2600
cellbender:remove-background: [epoch 062]  average training loss: 1159.7751
cellbender:remove-background: [epoch 063]  average training loss: 1155.5935
cellbender:remove-background: [epoch 064]  average training loss: 1157.4299
cellbender:remove-background: [epoch 065]  average training loss: 1157.9326
cellbender:remove-background: [epoch 065] average test loss: 1212.0217
cellbender:remove-background: [epoch 066]  average training loss: 1157.0688
cellbender:remove-background: [epoch 067]  average training loss: 1158.1910
cellbender:remove-background: [epoch 068]  average training loss: 1153.6795
cellbender:remove-background: [epoch 069]  average training loss: 1153.8084
cellbender:remove-background: [epoch 070]  average training loss: 1153.0683
cellbender:remove-background: [epoch 070] average test loss: 1220.8232
cellbender:remove-background: [epoch 071]  average training loss: 1154.4960
cellbender:remove-background: [epoch 072]  average training loss: 1153.6023
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/1734-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 073]  average training loss: 1151.2479
cellbender:remove-background: [epoch 074]  average training loss: 1155.0722
cellbender:remove-background: [epoch 075]  average training loss: 1150.6645
cellbender:remove-background: [epoch 075] average test loss: 1199.7884
cellbender:remove-background: [epoch 076]  average training loss: 1154.2462
cellbender:remove-background: [epoch 077]  average training loss: 1151.2865
cellbender:remove-background: [epoch 078]  average training loss: 1152.2916
cellbender:remove-background: [epoch 079]  average training loss: 1156.1949
cellbender:remove-background: [epoch 080]  average training loss: 1154.4771
cellbender:remove-background: [epoch 080] average test loss: 1216.7646
cellbender:remove-background: [epoch 081]  average training loss: 1155.4547
cellbender:remove-background: [epoch 082]  average training loss: 1154.1044
cellbender:remove-background: [epoch 083]  average training loss: 1152.9266
cellbender:remove-background: [epoch 084]  average training loss: 1154.6412
cellbender:remove-background: [epoch 085]  average training loss: 1154.5506
cellbender:remove-background: [epoch 085] average test loss: 1211.3424
cellbender:remove-background: [epoch 086]  average training loss: 1151.7035
cellbender:remove-background: [epoch 087]  average training loss: 1154.4472
cellbender:remove-background: [epoch 088]  average training loss: 1156.5058
cellbender:remove-background: [epoch 089]  average training loss: 1154.1388
cellbender:remove-background: [epoch 090]  average training loss: 1158.1204
cellbender:remove-background: [epoch 090] average test loss: 1223.9417
cellbender:remove-background: [epoch 091]  average training loss: 1153.5856
cellbender:remove-background: [epoch 092]  average training loss: 1150.9272
cellbender:remove-background: [epoch 093]  average training loss: 1154.5190
cellbender:remove-background: [epoch 094]  average training loss: 1155.7779
cellbender:remove-background: [epoch 095]  average training loss: 1152.5302
cellbender:remove-background: [epoch 095] average test loss: 1259.2497
cellbender:remove-background: [epoch 096]  average training loss: 1154.1019
cellbender:remove-background: [epoch 097]  average training loss: 1153.5340
cellbender:remove-background: [epoch 098]  average training loss: 1156.8686
cellbender:remove-background: [epoch 099]  average training loss: 1154.6872
cellbender:remove-background: [epoch 100]  average training loss: 1155.5572
cellbender:remove-background: [epoch 100] average test loss: 1212.1583
cellbender:remove-background: [epoch 101]  average training loss: 1154.1376
cellbender:remove-background: [epoch 102]  average training loss: 1155.5733
cellbender:remove-background: [epoch 103]  average training loss: 1154.6825
cellbender:remove-background: [epoch 104]  average training loss: 1153.2994
cellbender:remove-background: [epoch 105]  average training loss: 1155.3351
cellbender:remove-background: [epoch 105] average test loss: 1217.8640
cellbender:remove-background: [epoch 106]  average training loss: 1157.1899
cellbender:remove-background: [epoch 107]  average training loss: 1154.4160
cellbender:remove-background: [epoch 108]  average training loss: 1154.7832
cellbender:remove-background: [epoch 109]  average training loss: 1153.4776
cellbender:remove-background: [epoch 110]  average training loss: 1154.8354
cellbender:remove-background: [epoch 110] average test loss: 1221.9945
cellbender:remove-background: [epoch 111]  average training loss: 1155.6269
cellbender:remove-background: [epoch 112]  average training loss: 1155.3064
cellbender:remove-background: [epoch 113]  average training loss: 1154.6111
cellbender:remove-background: [epoch 114]  average training loss: 1154.4717
cellbender:remove-background: [epoch 115]  average training loss: 1153.4412
cellbender:remove-background: [epoch 115] average test loss: 1220.1067
cellbender:remove-background: [epoch 116]  average training loss: 1155.7411
cellbender:remove-background: [epoch 117]  average training loss: 1154.1366
cellbender:remove-background: [epoch 118]  average training loss: 1154.9073
cellbender:remove-background: [epoch 119]  average training loss: 1153.3019
cellbender:remove-background: [epoch 120]  average training loss: 1152.8490
cellbender:remove-background: [epoch 120] average test loss: 1218.7083
cellbender:remove-background: [epoch 121]  average training loss: 1154.2881
cellbender:remove-background: [epoch 122]  average training loss: 1153.2309
cellbender:remove-background: [epoch 123]  average training loss: 1153.7668
cellbender:remove-background: [epoch 124]  average training loss: 1154.1224
cellbender:remove-background: [epoch 125]  average training loss: 1154.9756
cellbender:remove-background: [epoch 125] average test loss: 1226.4820
cellbender:remove-background: [epoch 126]  average training loss: 1154.2590
cellbender:remove-background: [epoch 127]  average training loss: 1153.7502
cellbender:remove-background: [epoch 128]  average training loss: 1155.0917
cellbender:remove-background: [epoch 129]  average training loss: 1154.5607
cellbender:remove-background: [epoch 130]  average training loss: 1154.6345
cellbender:remove-background: [epoch 130] average test loss: 1223.3311
cellbender:remove-background: [epoch 131]  average training loss: 1154.5770
cellbender:remove-background: [epoch 132]  average training loss: 1154.1852
cellbender:remove-background: [epoch 133]  average training loss: 1154.8218
cellbender:remove-background: [epoch 134]  average training loss: 1152.5581
cellbender:remove-background: [epoch 135]  average training loss: 1154.3061
cellbender:remove-background: [epoch 135] average test loss: 1222.2516
cellbender:remove-background: [epoch 136]  average training loss: 1154.2543
cellbender:remove-background: [epoch 137]  average training loss: 1152.6476
cellbender:remove-background: [epoch 138]  average training loss: 1153.6313
cellbender:remove-background: [epoch 139]  average training loss: 1151.7127
cellbender:remove-background: [epoch 140]  average training loss: 1153.4685
cellbender:remove-background: [epoch 140] average test loss: 1224.6309
cellbender:remove-background: [epoch 141]  average training loss: 1152.3576
cellbender:remove-background: [epoch 142]  average training loss: 1153.5928
cellbender:remove-background: [epoch 143]  average training loss: 1152.8436
cellbender:remove-background: [epoch 144]  average training loss: 1154.0261
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/1734-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 145]  average training loss: 1153.1438
cellbender:remove-background: [epoch 145] average test loss: 1221.8214
cellbender:remove-background: [epoch 146]  average training loss: 1153.2686
cellbender:remove-background: [epoch 147]  average training loss: 1152.7644
cellbender:remove-background: [epoch 148]  average training loss: 1153.3514
cellbender:remove-background: [epoch 149]  average training loss: 1153.4610
cellbender:remove-background: [epoch 150]  average training loss: 1152.7375
cellbender:remove-background: [epoch 150] average test loss: 1220.6637
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/1734-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:10:41
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpwy10c5q6
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpwy10c5q6
/tmp/tmpwy10c5q6/a0031998c5_random.pyro
/tmp/tmpwy10c5q6/a0031998c5_random.cuda
/tmp/tmpwy10c5q6/a0031998c5_model.torch
/tmp/tmpwy10c5q6/a0031998c5_optim.torch
/tmp/tmpwy10c5q6/a0031998c5_optim.pyro
/tmp/tmpwy10c5q6/a0031998c5_params.pyro
/tmp/tmpwy10c5q6/a0031998c5_train.loaderstate
/tmp/tmpwy10c5q6/a0031998c5_test.loaderstate
/tmp/tmpwy10c5q6/a0031998c5_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 (1/42)
cellbender:remove-background:     [0.03 mins per chunk]
cellbender:remove-background: Working on chunk (2/42)
cellbender:remove-background: Working on chunk (3/42)
cellbender:remove-background: Working on chunk (4/42)
cellbender:remove-background: Working on chunk (5/42)
cellbender:remove-background: Working on chunk (6/42)
cellbender:remove-background: Working on chunk (7/42)
cellbender:remove-background: Working on chunk (8/42)
cellbender:remove-background: Working on chunk (9/42)
cellbender:remove-background: Working on chunk (10/42)
cellbender:remove-background: Working on chunk (11/42)
cellbender:remove-background: Working on chunk (12/42)
cellbender:remove-background: Working on chunk (13/42)
cellbender:remove-background: Working on chunk (14/42)
cellbender:remove-background: Working on chunk (15/42)
cellbender:remove-background: Working on chunk (16/42)
cellbender:remove-background: Working on chunk (17/42)
cellbender:remove-background: Working on chunk (18/42)
cellbender:remove-background: Working on chunk (19/42)
cellbender:remove-background: Working on chunk (20/42)
cellbender:remove-background: Working on chunk (21/42)
cellbender:remove-background: Working on chunk (22/42)
cellbender:remove-background: Working on chunk (23/42)
cellbender:remove-background: Working on chunk (24/42)
cellbender:remove-background: Working on chunk (25/42)
cellbender:remove-background: Working on chunk (26/42)
cellbender:remove-background: Working on chunk (27/42)
cellbender:remove-background: Working on chunk (28/42)
cellbender:remove-background: Working on chunk (29/42)
cellbender:remove-background: Working on chunk (30/42)
cellbender:remove-background: Working on chunk (31/42)
cellbender:remove-background: Working on chunk (32/42)
cellbender:remove-background: Working on chunk (33/42)
cellbender:remove-background: Working on chunk (34/42)
cellbender:remove-background: Working on chunk (35/42)
cellbender:remove-background: Working on chunk (36/42)
cellbender:remove-background: Working on chunk (37/42)
cellbender:remove-background: Working on chunk (38/42)
cellbender:remove-background: Working on chunk (39/42)
cellbender:remove-background: Working on chunk (40/42)
cellbender:remove-background: Working on chunk (41/42)
cellbender:remove-background: Working on chunk (42/42)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1734-Bipolar-dACC/1734-Bipolar-dACC.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/1734-Bipolar-dACC/1734-Bipolar-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:13:31

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1734-Bipolar-dACC/1734-Bipolar-dACC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1734-Bipolar-dACC/1734-Bipolar-dACC.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:     [0.64 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 15:18:10 Total MCKP estimation time = 267.63 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/1734-Bipolar-dACC/1734-Bipolar-dACC.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/1734-Bipolar-dACC/1734-Bipolar-dACC.cellbender.output_filtered.h5
cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1734-Bipolar-dACC/1734-Bipolar-dACC.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/1734-Bipolar-dACC/1734-Bipolar-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:18:20