cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2797-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-Hippocampus/2797-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 5021 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 4918f41172)
cellbender:remove-background: 2024-06-06 15:42:01
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/2797-Schizophrenia-Hippocampus.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: 30112 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 981
cellbender:remove-background: Prior on counts for empty droplets is 37
cellbender:remove-background: Excluding 10397 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 19715 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 18
cellbender:remove-background: Using 5021 probable cell barcodes, plus an additional 14979 barcodes, and 44485 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 37 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpzigewu1s
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: 1685.6071
cellbender:remove-background: [epoch 002]  average training loss: 1467.5615  (11.4 seconds per epoch)
cellbender:remove-background: Will checkpoint every 37 epochs
cellbender:remove-background: [epoch 003]  average training loss: 1370.3960
cellbender:remove-background: [epoch 004]  average training loss: 1282.9692
cellbender:remove-background: [epoch 005]  average training loss: 1262.7477
cellbender:remove-background: [epoch 005] average test loss: 1298.8049
cellbender:remove-background: [epoch 006]  average training loss: 1256.7446
cellbender:remove-background: [epoch 007]  average training loss: 1238.5308
cellbender:remove-background: [epoch 008]  average training loss: 1233.6525
cellbender:remove-background: [epoch 009]  average training loss: 1235.5365
cellbender:remove-background: [epoch 010]  average training loss: 1222.5817
cellbender:remove-background: [epoch 010] average test loss: 1243.5689
cellbender:remove-background: [epoch 011]  average training loss: 1223.0988
cellbender:remove-background: [epoch 012]  average training loss: 1214.6142
cellbender:remove-background: [epoch 013]  average training loss: 1180.6337
cellbender:remove-background: [epoch 014]  average training loss: 1174.8317
cellbender:remove-background: [epoch 015]  average training loss: 1163.3517
cellbender:remove-background: [epoch 015] average test loss: 1187.8321
cellbender:remove-background: [epoch 016]  average training loss: 1155.6190
cellbender:remove-background: [epoch 017]  average training loss: 1158.5170
cellbender:remove-background: [epoch 018]  average training loss: 1151.9623
cellbender:remove-background: [epoch 019]  average training loss: 1145.6021
cellbender:remove-background: [epoch 020]  average training loss: 1140.7721
cellbender:remove-background: [epoch 020] average test loss: 1166.9999
cellbender:remove-background: [epoch 021]  average training loss: 1141.3980
cellbender:remove-background: [epoch 022]  average training loss: 1140.1201
cellbender:remove-background: [epoch 023]  average training loss: 1139.2742
cellbender:remove-background: [epoch 024]  average training loss: 1135.2688
cellbender:remove-background: [epoch 025]  average training loss: 1135.0549
cellbender:remove-background: [epoch 025] average test loss: 1164.4513
cellbender:remove-background: [epoch 026]  average training loss: 1122.9470
cellbender:remove-background: [epoch 027]  average training loss: 1118.0743
cellbender:remove-background: [epoch 028]  average training loss: 1117.0393
cellbender:remove-background: [epoch 029]  average training loss: 1110.7153
cellbender:remove-background: [epoch 030]  average training loss: 1107.8535
cellbender:remove-background: [epoch 030] average test loss: 1130.6172
cellbender:remove-background: [epoch 031]  average training loss: 1105.5123
cellbender:remove-background: [epoch 032]  average training loss: 1103.0508
cellbender:remove-background: [epoch 033]  average training loss: 1101.0031
cellbender:remove-background: [epoch 034]  average training loss: 1098.4362
cellbender:remove-background: [epoch 035]  average training loss: 1096.8418
cellbender:remove-background: [epoch 035] average test loss: 1122.8180
cellbender:remove-background: [epoch 036]  average training loss: 1094.4547
cellbender:remove-background: [epoch 037]  average training loss: 1094.0480
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/2797-Schizophrenia-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 038]  average training loss: 1094.4478
cellbender:remove-background: [epoch 039]  average training loss: 1091.9771
cellbender:remove-background: [epoch 040]  average training loss: 1089.1595
cellbender:remove-background: [epoch 040] average test loss: 1112.0342
cellbender:remove-background: [epoch 041]  average training loss: 1094.2334
cellbender:remove-background: [epoch 042]  average training loss: 1100.8219
cellbender:remove-background: [epoch 043]  average training loss: 1105.6321
cellbender:remove-background: [epoch 044]  average training loss: 1096.3580
cellbender:remove-background: [epoch 045]  average training loss: 1113.0688
cellbender:remove-background: [epoch 045] average test loss: 1128.5288
cellbender:remove-background: [epoch 046]  average training loss: 1108.2494
cellbender:remove-background: [epoch 047]  average training loss: 1110.2015
cellbender:remove-background: [epoch 048]  average training loss: 1107.5143
cellbender:remove-background: [epoch 049]  average training loss: 1112.9555
cellbender:remove-background: [epoch 050]  average training loss: 1112.3560
cellbender:remove-background: [epoch 050] average test loss: 1149.2959
cellbender:remove-background: [epoch 051]  average training loss: 1112.2785
cellbender:remove-background: [epoch 052]  average training loss: 1115.1243
cellbender:remove-background: [epoch 053]  average training loss: 1113.7903
cellbender:remove-background: [epoch 054]  average training loss: 1106.8849
cellbender:remove-background: [epoch 055]  average training loss: 1116.9404
cellbender:remove-background: [epoch 055] average test loss: 1146.1262
cellbender:remove-background: [epoch 056]  average training loss: 1116.8661
cellbender:remove-background: [epoch 057]  average training loss: 1120.8400
cellbender:remove-background: [epoch 058]  average training loss: 1115.0635
cellbender:remove-background: [epoch 059]  average training loss: 1112.6748
cellbender:remove-background: [epoch 060]  average training loss: 1120.6537
cellbender:remove-background: [epoch 060] average test loss: 1152.0170
cellbender:remove-background: [epoch 061]  average training loss: 1115.3587
cellbender:remove-background: [epoch 062]  average training loss: 1117.6186
cellbender:remove-background: [epoch 063]  average training loss: 1117.5619
cellbender:remove-background: [epoch 064]  average training loss: 1120.0735
cellbender:remove-background: [epoch 065]  average training loss: 1114.9743
cellbender:remove-background: [epoch 065] average test loss: 1148.4566
cellbender:remove-background: [epoch 066]  average training loss: 1116.6112
cellbender:remove-background: [epoch 067]  average training loss: 1112.3382
cellbender:remove-background: [epoch 068]  average training loss: 1110.0561
cellbender:remove-background: [epoch 069]  average training loss: 1114.1868
cellbender:remove-background: [epoch 070]  average training loss: 1118.7687
cellbender:remove-background: [epoch 070] average test loss: 1164.6313
cellbender:remove-background: [epoch 071]  average training loss: 1112.1558
cellbender:remove-background: [epoch 072]  average training loss: 1113.5428
cellbender:remove-background: [epoch 073]  average training loss: 1113.0498
cellbender:remove-background: [epoch 074]  average training loss: 1108.2196
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/2797-Schizophrenia-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 075]  average training loss: 1111.4879
cellbender:remove-background: [epoch 075] average test loss: 1148.1801
cellbender:remove-background: [epoch 076]  average training loss: 1111.1330
cellbender:remove-background: [epoch 077]  average training loss: 1113.9451
cellbender:remove-background: [epoch 078]  average training loss: 1110.8461
cellbender:remove-background: [epoch 079]  average training loss: 1113.6372
cellbender:remove-background: [epoch 080]  average training loss: 1108.6240
cellbender:remove-background: [epoch 080] average test loss: 1167.5844
cellbender:remove-background: [epoch 081]  average training loss: 1115.4866
cellbender:remove-background: [epoch 082]  average training loss: 1109.6284
cellbender:remove-background: [epoch 083]  average training loss: 1110.9767
cellbender:remove-background: [epoch 084]  average training loss: 1111.7239
cellbender:remove-background: [epoch 085]  average training loss: 1113.8428
cellbender:remove-background: [epoch 085] average test loss: 1146.0990
cellbender:remove-background: [epoch 086]  average training loss: 1112.4593
cellbender:remove-background: [epoch 087]  average training loss: 1108.9501
cellbender:remove-background: [epoch 088]  average training loss: 1109.3090
cellbender:remove-background: [epoch 089]  average training loss: 1105.0758
cellbender:remove-background: [epoch 090]  average training loss: 1106.3158
cellbender:remove-background: [epoch 090] average test loss: 1168.5676
cellbender:remove-background: [epoch 091]  average training loss: 1106.6262
cellbender:remove-background: [epoch 092]  average training loss: 1110.7488
cellbender:remove-background: [epoch 093]  average training loss: 1109.3566
cellbender:remove-background: [epoch 094]  average training loss: 1109.0619
cellbender:remove-background: [epoch 095]  average training loss: 1106.4044
cellbender:remove-background: [epoch 095] average test loss: 1165.0945
cellbender:remove-background: [epoch 096]  average training loss: 1104.9582
cellbender:remove-background: [epoch 097]  average training loss: 1108.8253
cellbender:remove-background: [epoch 098]  average training loss: 1111.4473
cellbender:remove-background: [epoch 099]  average training loss: 1109.9522
cellbender:remove-background: [epoch 100]  average training loss: 1105.3504
cellbender:remove-background: [epoch 100] average test loss: 1148.2380
cellbender:remove-background: [epoch 101]  average training loss: 1105.0240
cellbender:remove-background: [epoch 102]  average training loss: 1103.7950
cellbender:remove-background: [epoch 103]  average training loss: 1104.2429
cellbender:remove-background: [epoch 104]  average training loss: 1102.3778
cellbender:remove-background: [epoch 105]  average training loss: 1105.0190
cellbender:remove-background: [epoch 105] average test loss: 1155.3669
cellbender:remove-background: [epoch 106]  average training loss: 1103.0663
cellbender:remove-background: [epoch 107]  average training loss: 1101.7341
cellbender:remove-background: [epoch 108]  average training loss: 1104.7406
cellbender:remove-background: [epoch 109]  average training loss: 1104.6889
cellbender:remove-background: [epoch 110]  average training loss: 1100.6998
cellbender:remove-background: [epoch 110] average test loss: 1159.0828
cellbender:remove-background: [epoch 111]  average training loss: 1105.8041
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/2797-Schizophrenia-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 112]  average training loss: 1103.1935
cellbender:remove-background: [epoch 113]  average training loss: 1097.7641
cellbender:remove-background: [epoch 114]  average training loss: 1100.0897
cellbender:remove-background: [epoch 115]  average training loss: 1102.3207
cellbender:remove-background: [epoch 115] average test loss: 1152.9052
cellbender:remove-background: [epoch 116]  average training loss: 1103.5577
cellbender:remove-background: [epoch 117]  average training loss: 1102.6609
cellbender:remove-background: [epoch 118]  average training loss: 1100.2088
cellbender:remove-background: [epoch 119]  average training loss: 1102.2412
cellbender:remove-background: [epoch 120]  average training loss: 1102.1996
cellbender:remove-background: [epoch 120] average test loss: 1154.1253
cellbender:remove-background: [epoch 121]  average training loss: 1100.5277
cellbender:remove-background: [epoch 122]  average training loss: 1099.5833
cellbender:remove-background: [epoch 123]  average training loss: 1098.7743
cellbender:remove-background: [epoch 124]  average training loss: 1099.2269
cellbender:remove-background: [epoch 125]  average training loss: 1100.4475
cellbender:remove-background: [epoch 125] average test loss: 1157.7180
cellbender:remove-background: [epoch 126]  average training loss: 1098.8485
cellbender:remove-background: [epoch 127]  average training loss: 1098.4858
cellbender:remove-background: [epoch 128]  average training loss: 1099.5430
cellbender:remove-background: [epoch 129]  average training loss: 1100.8887
cellbender:remove-background: [epoch 130]  average training loss: 1100.3058
cellbender:remove-background: [epoch 130] average test loss: 1147.9650
cellbender:remove-background: [epoch 131]  average training loss: 1098.8146
cellbender:remove-background: [epoch 132]  average training loss: 1099.7922
cellbender:remove-background: [epoch 133]  average training loss: 1101.0765
cellbender:remove-background: [epoch 134]  average training loss: 1099.9954
cellbender:remove-background: [epoch 135]  average training loss: 1097.7505
cellbender:remove-background: [epoch 135] average test loss: 1148.9408
cellbender:remove-background: [epoch 136]  average training loss: 1100.0139
cellbender:remove-background: [epoch 137]  average training loss: 1098.8178
cellbender:remove-background: [epoch 138]  average training loss: 1100.7276
cellbender:remove-background: [epoch 139]  average training loss: 1097.5524
cellbender:remove-background: [epoch 140]  average training loss: 1098.7548
cellbender:remove-background: [epoch 140] average test loss: 1156.8473
cellbender:remove-background: [epoch 141]  average training loss: 1098.2867
cellbender:remove-background: [epoch 142]  average training loss: 1099.9758
cellbender:remove-background: [epoch 143]  average training loss: 1099.7028
cellbender:remove-background: [epoch 144]  average training loss: 1098.1959
cellbender:remove-background: [epoch 145]  average training loss: 1097.8600
cellbender:remove-background: [epoch 145] average test loss: 1154.7864
cellbender:remove-background: [epoch 146]  average training loss: 1098.3166
cellbender:remove-background: [epoch 147]  average training loss: 1098.4687
cellbender:remove-background: [epoch 148]  average training loss: 1098.2371
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/2797-Schizophrenia-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 149]  average training loss: 1096.9142
cellbender:remove-background: [epoch 150]  average training loss: 1098.0953
cellbender:remove-background: [epoch 150] average test loss: 1149.9203
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/2797-Schizophrenia-Hippocampus/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 16:19:38
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmplfamox_r
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmplfamox_r
/tmp/tmplfamox_r/4918f41172_random.pyro
/tmp/tmplfamox_r/4918f41172_random.cuda
/tmp/tmplfamox_r/4918f41172_model.torch
/tmp/tmplfamox_r/4918f41172_optim.torch
/tmp/tmplfamox_r/4918f41172_optim.pyro
/tmp/tmplfamox_r/4918f41172_params.pyro
/tmp/tmplfamox_r/4918f41172_train.loaderstate
/tmp/tmplfamox_r/4918f41172_test.loaderstate
/tmp/tmplfamox_r/4918f41172_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 (1/52)
cellbender:remove-background:     [0.11 mins per chunk]
cellbender:remove-background: Working on chunk (2/52)
cellbender:remove-background: Working on chunk (3/52)
cellbender:remove-background: Working on chunk (4/52)
cellbender:remove-background: Working on chunk (5/52)
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cellbender:remove-background: Working on chunk (21/52)
cellbender:remove-background: Working on chunk (22/52)
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cellbender:remove-background: Working on chunk (25/52)
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cellbender:remove-background: Working on chunk (27/52)
cellbender:remove-background: Working on chunk (28/52)
cellbender:remove-background: Working on chunk (29/52)
cellbender:remove-background: Working on chunk (30/52)
cellbender:remove-background: Working on chunk (31/52)
cellbender:remove-background: Working on chunk (32/52)
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cellbender:remove-background: Working on chunk (36/52)
cellbender:remove-background: Working on chunk (37/52)
cellbender:remove-background: Working on chunk (38/52)
cellbender:remove-background: Working on chunk (39/52)
cellbender:remove-background: Working on chunk (40/52)
cellbender:remove-background: Working on chunk (41/52)
cellbender:remove-background: Working on chunk (42/52)
cellbender:remove-background: Working on chunk (43/52)
cellbender:remove-background: Working on chunk (44/52)
cellbender:remove-background: Working on chunk (45/52)
cellbender:remove-background: Working on chunk (46/52)
cellbender:remove-background: Working on chunk (47/52)
cellbender:remove-background: Working on chunk (48/52)
cellbender:remove-background: Working on chunk (49/52)
cellbender:remove-background: Working on chunk (50/52)
cellbender:remove-background: Working on chunk (51/52)
cellbender:remove-background: Working on chunk (52/52)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-Hippocampus/2797-Schizophrenia-Hippocampus.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/2797-Schizophrenia-Hippocampus/2797-Schizophrenia-Hippocampus.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 16:26:59

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-Hippocampus/2797-Schizophrenia-Hippocampus.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-Hippocampus/2797-Schizophrenia-Hippocampus.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:     [1.34 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 16:36:41 Total MCKP estimation time = 559.68 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/2797-Schizophrenia-Hippocampus/2797-Schizophrenia-Hippocampus.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/2797-Schizophrenia-Hippocampus/2797-Schizophrenia-Hippocampus.cellbender.output_filtered.h5
cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-Hippocampus/2797-Schizophrenia-Hippocampus.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/2797-Schizophrenia-Hippocampus/2797-Schizophrenia-Hippocampus.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 16:37:01