cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2686-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2686-Bipolar-dACC/2686-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 5450 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 4afc88303d)
cellbender:remove-background: 2024-06-06 15:05:06
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/2686-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: 32676 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 8979
cellbender:remove-background: Prior on counts for empty droplets is 72
cellbender:remove-background: Excluding 10540 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 22136 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 36
cellbender:remove-background: Using 5450 probable cell barcodes, plus an additional 14550 barcodes, and 50888 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 72 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp267_5ea2
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: 8491.7953
cellbender:remove-background: [epoch 002]  average training loss: 5809.8759  (7.3 seconds per epoch)
cellbender:remove-background: Will checkpoint every 58 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4445.9786
cellbender:remove-background: [epoch 004]  average training loss: 3913.2396
cellbender:remove-background: [epoch 005]  average training loss: 3772.9386
cellbender:remove-background: [epoch 005] average test loss: 3925.2147
cellbender:remove-background: [epoch 006]  average training loss: 3746.2036
cellbender:remove-background: [epoch 007]  average training loss: 3690.0785
cellbender:remove-background: [epoch 008]  average training loss: 3653.8521
cellbender:remove-background: [epoch 009]  average training loss: 3633.1740
cellbender:remove-background: [epoch 010]  average training loss: 3562.1759
cellbender:remove-background: [epoch 010] average test loss: 3544.5255
cellbender:remove-background: [epoch 011]  average training loss: 3438.0193
cellbender:remove-background: [epoch 012]  average training loss: 3319.5843
cellbender:remove-background: [epoch 013]  average training loss: 3269.0825
cellbender:remove-background: [epoch 014]  average training loss: 3275.7356
cellbender:remove-background: [epoch 015]  average training loss: 3212.1020
cellbender:remove-background: [epoch 015] average test loss: 3262.9591
cellbender:remove-background: [epoch 016]  average training loss: 3189.0962
cellbender:remove-background: [epoch 017]  average training loss: 3195.3967
cellbender:remove-background: [epoch 018]  average training loss: 3171.9575
cellbender:remove-background: [epoch 019]  average training loss: 3144.0326
cellbender:remove-background: [epoch 020]  average training loss: 3099.1816
cellbender:remove-background: [epoch 020] average test loss: 3107.2879
cellbender:remove-background: [epoch 021]  average training loss: 3070.8893
cellbender:remove-background: [epoch 022]  average training loss: 3054.0197
cellbender:remove-background: [epoch 023]  average training loss: 3046.9515
cellbender:remove-background: [epoch 024]  average training loss: 3030.2854
cellbender:remove-background: [epoch 025]  average training loss: 3022.2424
cellbender:remove-background: [epoch 025] average test loss: 3013.4841
cellbender:remove-background: [epoch 026]  average training loss: 3006.6435
cellbender:remove-background: [epoch 027]  average training loss: 2997.7167
cellbender:remove-background: [epoch 028]  average training loss: 2991.4990
cellbender:remove-background: [epoch 029]  average training loss: 2984.4227
cellbender:remove-background: [epoch 030]  average training loss: 2979.5821
cellbender:remove-background: [epoch 030] average test loss: 2959.8465
cellbender:remove-background: [epoch 031]  average training loss: 2975.9566
cellbender:remove-background: [epoch 032]  average training loss: 2970.9371
cellbender:remove-background: [epoch 033]  average training loss: 2968.0086
cellbender:remove-background: [epoch 034]  average training loss: 2964.9347
cellbender:remove-background: [epoch 035]  average training loss: 2962.5853
cellbender:remove-background: [epoch 035] average test loss: 2935.1337
cellbender:remove-background: [epoch 036]  average training loss: 2962.8178
cellbender:remove-background: [epoch 037]  average training loss: 2958.6556
cellbender:remove-background: [epoch 038]  average training loss: 2956.4028
cellbender:remove-background: [epoch 039]  average training loss: 2954.5077
cellbender:remove-background: [epoch 040]  average training loss: 2950.8713
cellbender:remove-background: [epoch 040] average test loss: 2933.2987
cellbender:remove-background: [epoch 041]  average training loss: 2949.9858
cellbender:remove-background: [epoch 042]  average training loss: 2944.0960
cellbender:remove-background: [epoch 043]  average training loss: 2944.5952
cellbender:remove-background: [epoch 044]  average training loss: 2958.5213
cellbender:remove-background: [epoch 045]  average training loss: 2940.0734
cellbender:remove-background: [epoch 045] average test loss: 2918.6827
cellbender:remove-background: [epoch 046]  average training loss: 2937.9841
cellbender:remove-background: [epoch 047]  average training loss: 2934.9573
cellbender:remove-background: [epoch 048]  average training loss: 2932.9818
cellbender:remove-background: [epoch 049]  average training loss: 2930.2746
cellbender:remove-background: [epoch 050]  average training loss: 2933.9894
cellbender:remove-background: [epoch 050] average test loss: 2918.4107
cellbender:remove-background: [epoch 051]  average training loss: 2927.5797
cellbender:remove-background: [epoch 052]  average training loss: 2925.9797
cellbender:remove-background: [epoch 053]  average training loss: 2925.3303
cellbender:remove-background: [epoch 054]  average training loss: 2922.1441
cellbender:remove-background: [epoch 055]  average training loss: 2922.2327
cellbender:remove-background: [epoch 055] average test loss: 2914.3953
cellbender:remove-background: [epoch 056]  average training loss: 2919.1999
cellbender:remove-background: [epoch 057]  average training loss: 2920.8296
cellbender:remove-background: [epoch 058]  average training loss: 2917.7738
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/2686-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 059]  average training loss: 2916.5806
cellbender:remove-background: [epoch 060]  average training loss: 2913.7611
cellbender:remove-background: [epoch 060] average test loss: 2902.8534
cellbender:remove-background: [epoch 061]  average training loss: 2913.3857
cellbender:remove-background: [epoch 062]  average training loss: 2913.6708
cellbender:remove-background: [epoch 063]  average training loss: 2914.7250
cellbender:remove-background: [epoch 064]  average training loss: 2914.7093
cellbender:remove-background: [epoch 065]  average training loss: 2912.0626
cellbender:remove-background: [epoch 065] average test loss: 2899.4427
cellbender:remove-background: [epoch 066]  average training loss: 2914.1318
cellbender:remove-background: [epoch 067]  average training loss: 2914.2643
cellbender:remove-background: [epoch 068]  average training loss: 2915.6952
cellbender:remove-background: [epoch 069]  average training loss: 2916.1490
cellbender:remove-background: [epoch 070]  average training loss: 2917.1691
cellbender:remove-background: [epoch 070] average test loss: 2905.2246
cellbender:remove-background: [epoch 071]  average training loss: 2914.2746
cellbender:remove-background: [epoch 072]  average training loss: 2915.8676
cellbender:remove-background: [epoch 073]  average training loss: 2915.7279
cellbender:remove-background: [epoch 074]  average training loss: 2915.4301
cellbender:remove-background: [epoch 075]  average training loss: 2918.9174
cellbender:remove-background: [epoch 075] average test loss: 2912.1658
cellbender:remove-background: [epoch 076]  average training loss: 2915.0597
cellbender:remove-background: [epoch 077]  average training loss: 2913.5272
cellbender:remove-background: [epoch 078]  average training loss: 2918.9732
cellbender:remove-background: [epoch 079]  average training loss: 2918.3159
cellbender:remove-background: [epoch 080]  average training loss: 2921.5027
cellbender:remove-background: [epoch 080] average test loss: 2917.1738
cellbender:remove-background: [epoch 081]  average training loss: 2925.2184
cellbender:remove-background: [epoch 082]  average training loss: 2920.6776
cellbender:remove-background: [epoch 083]  average training loss: 2921.8816
cellbender:remove-background: [epoch 084]  average training loss: 2917.0197
cellbender:remove-background: [epoch 085]  average training loss: 2917.0046
cellbender:remove-background: [epoch 085] average test loss: 2938.4411
cellbender:remove-background: [epoch 086]  average training loss: 2916.7746
cellbender:remove-background: [epoch 087]  average training loss: 2921.6390
cellbender:remove-background: [epoch 088]  average training loss: 2915.8358
cellbender:remove-background: [epoch 089]  average training loss: 2919.5001
cellbender:remove-background: [epoch 090]  average training loss: 2923.4514
cellbender:remove-background: [epoch 090] average test loss: 2958.7929
cellbender:remove-background: [epoch 091]  average training loss: 2922.6018
cellbender:remove-background: [epoch 092]  average training loss: 2920.4746
cellbender:remove-background: [epoch 093]  average training loss: 2924.4894
cellbender:remove-background: [epoch 094]  average training loss: 2920.8343
cellbender:remove-background: [epoch 095]  average training loss: 2920.5748
cellbender:remove-background: [epoch 095] average test loss: 2935.5952
cellbender:remove-background: [epoch 096]  average training loss: 2923.0883
cellbender:remove-background: [epoch 097]  average training loss: 2920.3182
cellbender:remove-background: [epoch 098]  average training loss: 2920.2771
cellbender:remove-background: [epoch 099]  average training loss: 2917.0524
cellbender:remove-background: [epoch 100]  average training loss: 2915.8872
cellbender:remove-background: [epoch 100] average test loss: 2926.2239
cellbender:remove-background: [epoch 101]  average training loss: 2916.4692
cellbender:remove-background: [epoch 102]  average training loss: 2917.9031
cellbender:remove-background: [epoch 103]  average training loss: 2916.7979
cellbender:remove-background: [epoch 104]  average training loss: 2919.5550
cellbender:remove-background: [epoch 105]  average training loss: 2918.5741
cellbender:remove-background: [epoch 105] average test loss: 2942.0591
cellbender:remove-background: [epoch 106]  average training loss: 2918.7741
cellbender:remove-background: [epoch 107]  average training loss: 2918.8171
cellbender:remove-background: [epoch 108]  average training loss: 2918.1229
cellbender:remove-background: [epoch 109]  average training loss: 2915.3921
cellbender:remove-background: [epoch 110]  average training loss: 2918.6336
cellbender:remove-background: [epoch 110] average test loss: 2936.3715
cellbender:remove-background: [epoch 111]  average training loss: 2919.2920
cellbender:remove-background: [epoch 112]  average training loss: 2917.5988
cellbender:remove-background: [epoch 113]  average training loss: 2917.3487
cellbender:remove-background: [epoch 114]  average training loss: 2918.8275
cellbender:remove-background: [epoch 115]  average training loss: 2917.9311
cellbender:remove-background: [epoch 115] average test loss: 2939.9726
cellbender:remove-background: [epoch 116]  average training loss: 2916.6444
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/2686-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 117]  average training loss: 2919.5629
cellbender:remove-background: [epoch 118]  average training loss: 2916.9018
cellbender:remove-background: [epoch 119]  average training loss: 2914.3322
cellbender:remove-background: [epoch 120]  average training loss: 2914.0481
cellbender:remove-background: [epoch 120] average test loss: 2945.7896
cellbender:remove-background: [epoch 121]  average training loss: 2916.4566
cellbender:remove-background: [epoch 122]  average training loss: 2918.1513
cellbender:remove-background: [epoch 123]  average training loss: 2917.6884
cellbender:remove-background: [epoch 124]  average training loss: 2915.7456
cellbender:remove-background: [epoch 125]  average training loss: 2914.2151
cellbender:remove-background: [epoch 125] average test loss: 2947.4050
cellbender:remove-background: [epoch 126]  average training loss: 2918.2293
cellbender:remove-background: [epoch 127]  average training loss: 2913.9383
cellbender:remove-background: [epoch 128]  average training loss: 2917.5119
cellbender:remove-background: [epoch 129]  average training loss: 2916.6131
cellbender:remove-background: [epoch 130]  average training loss: 2916.1872
cellbender:remove-background: [epoch 130] average test loss: 2944.2323
cellbender:remove-background: [epoch 131]  average training loss: 2911.6733
cellbender:remove-background: [epoch 132]  average training loss: 2916.3492
cellbender:remove-background: [epoch 133]  average training loss: 2915.7286
cellbender:remove-background: [epoch 134]  average training loss: 2916.2445
cellbender:remove-background: [epoch 135]  average training loss: 2915.3343
cellbender:remove-background: [epoch 135] average test loss: 2942.6543
cellbender:remove-background: [epoch 136]  average training loss: 2915.0045
cellbender:remove-background: [epoch 137]  average training loss: 2918.9633
cellbender:remove-background: [epoch 138]  average training loss: 2914.6889
cellbender:remove-background: [epoch 139]  average training loss: 2915.3668
cellbender:remove-background: [epoch 140]  average training loss: 2913.6025
cellbender:remove-background: [epoch 140] average test loss: 2939.0529
cellbender:remove-background: [epoch 141]  average training loss: 2913.6503
cellbender:remove-background: [epoch 142]  average training loss: 2915.1702
cellbender:remove-background: [epoch 143]  average training loss: 2912.6407
cellbender:remove-background: [epoch 144]  average training loss: 2913.3429
cellbender:remove-background: [epoch 145]  average training loss: 2913.6101
cellbender:remove-background: [epoch 145] average test loss: 2943.8423
cellbender:remove-background: [epoch 146]  average training loss: 2914.1376
cellbender:remove-background: [epoch 147]  average training loss: 2912.9402
cellbender:remove-background: [epoch 148]  average training loss: 2914.1143
cellbender:remove-background: [epoch 149]  average training loss: 2913.8348
cellbender:remove-background: [epoch 150]  average training loss: 2914.3711
cellbender:remove-background: [epoch 150] average test loss: 2942.2990
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/2686-Bipolar-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:26:50
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpxa0y4rao
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpxa0y4rao
/tmp/tmpxa0y4rao/4afc88303d_random.pyro
/tmp/tmpxa0y4rao/4afc88303d_random.cuda
/tmp/tmpxa0y4rao/4afc88303d_model.torch
/tmp/tmpxa0y4rao/4afc88303d_optim.torch
/tmp/tmpxa0y4rao/4afc88303d_optim.pyro
/tmp/tmpxa0y4rao/4afc88303d_params.pyro
/tmp/tmpxa0y4rao/4afc88303d_train.loaderstate
/tmp/tmpxa0y4rao/4afc88303d_test.loaderstate
/tmp/tmpxa0y4rao/4afc88303d_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 (1/48)
cellbender:remove-background:     [0.04 mins per chunk]
cellbender:remove-background: Working on chunk (2/48)
cellbender:remove-background: Working on chunk (3/48)
cellbender:remove-background: Working on chunk (4/48)
cellbender:remove-background: Working on chunk (5/48)
cellbender:remove-background: Working on chunk (6/48)
cellbender:remove-background: Working on chunk (7/48)
cellbender:remove-background: Working on chunk (8/48)
cellbender:remove-background: Working on chunk (9/48)
cellbender:remove-background: Working on chunk (10/48)
cellbender:remove-background: Working on chunk (11/48)
cellbender:remove-background: Working on chunk (12/48)
cellbender:remove-background: Working on chunk (13/48)
cellbender:remove-background: Working on chunk (14/48)
cellbender:remove-background: Working on chunk (15/48)
cellbender:remove-background: Working on chunk (16/48)
cellbender:remove-background: Working on chunk (17/48)
cellbender:remove-background: Working on chunk (18/48)
cellbender:remove-background: Working on chunk (19/48)
cellbender:remove-background: Working on chunk (20/48)
cellbender:remove-background: Working on chunk (21/48)
cellbender:remove-background: Working on chunk (22/48)
cellbender:remove-background: Working on chunk (23/48)
cellbender:remove-background: Working on chunk (24/48)
cellbender:remove-background: Working on chunk (25/48)
cellbender:remove-background: Working on chunk (26/48)
cellbender:remove-background: Working on chunk (27/48)
cellbender:remove-background: Working on chunk (28/48)
cellbender:remove-background: Working on chunk (29/48)
cellbender:remove-background: Working on chunk (30/48)
cellbender:remove-background: Working on chunk (31/48)
cellbender:remove-background: Working on chunk (32/48)
cellbender:remove-background: Working on chunk (33/48)
cellbender:remove-background: Working on chunk (34/48)
cellbender:remove-background: Working on chunk (35/48)
cellbender:remove-background: Working on chunk (36/48)
cellbender:remove-background: Working on chunk (37/48)
cellbender:remove-background: Working on chunk (38/48)
cellbender:remove-background: Working on chunk (39/48)
cellbender:remove-background: Working on chunk (40/48)
cellbender:remove-background: Working on chunk (41/48)
cellbender:remove-background: Working on chunk (42/48)
cellbender:remove-background: Working on chunk (43/48)
cellbender:remove-background: Working on chunk (44/48)
cellbender:remove-background: Working on chunk (45/48)
cellbender:remove-background: Working on chunk (46/48)
cellbender:remove-background: Working on chunk (47/48)
cellbender:remove-background: Working on chunk (48/48)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2686-Bipolar-dACC/2686-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/2686-Bipolar-dACC/2686-Bipolar-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:31:03

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2686-Bipolar-dACC/2686-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/2686-Bipolar-dACC/2686-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:     [2.02 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 15:46:01 Total MCKP estimation time = 867.37 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/2686-Bipolar-dACC/2686-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/2686-Bipolar-dACC/2686-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/2686-Bipolar-dACC/2686-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/2686-Bipolar-dACC/2686-Bipolar-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:46:23