cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1838-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1838-Bipolar-DLPFC/1838-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 6054 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 4ddd6cde6f)
cellbender:remove-background: 2024-06-06 15:31:25
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/1838-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: 32348 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 6030
cellbender:remove-background: Prior on counts for empty droplets is 68
cellbender:remove-background: Excluding 11185 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 21163 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 34
cellbender:remove-background: Using 6054 probable cell barcodes, plus an additional 13946 barcodes, and 49211 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 67 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpy1om2hwz
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: 6443.0958
cellbender:remove-background: [epoch 002]  average training loss: 4787.4151  (5.2 seconds per epoch)
cellbender:remove-background: Will checkpoint every 81 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4000.2137
cellbender:remove-background: [epoch 004]  average training loss: 3561.4516
cellbender:remove-background: [epoch 005]  average training loss: 3447.6353
cellbender:remove-background: [epoch 005] average test loss: 3487.2718
cellbender:remove-background: [epoch 006]  average training loss: 3402.0789
cellbender:remove-background: [epoch 007]  average training loss: 3350.4211
cellbender:remove-background: [epoch 008]  average training loss: 3322.1556
cellbender:remove-background: [epoch 009]  average training loss: 3310.8032
cellbender:remove-background: [epoch 010]  average training loss: 3235.1786
cellbender:remove-background: [epoch 010] average test loss: 3220.0561
cellbender:remove-background: [epoch 011]  average training loss: 3170.2626
cellbender:remove-background: [epoch 012]  average training loss: 3133.1417
cellbender:remove-background: [epoch 013]  average training loss: 3110.6422
cellbender:remove-background: [epoch 014]  average training loss: 3122.9728
cellbender:remove-background: [epoch 015]  average training loss: 3092.1240
cellbender:remove-background: [epoch 015] average test loss: 3087.5015
cellbender:remove-background: [epoch 016]  average training loss: 3089.8744
cellbender:remove-background: [epoch 017]  average training loss: 3095.8868
cellbender:remove-background: [epoch 018]  average training loss: 3085.7873
cellbender:remove-background: [epoch 019]  average training loss: 3074.6013
cellbender:remove-background: [epoch 020]  average training loss: 3054.6604
cellbender:remove-background: [epoch 020] average test loss: 3027.1373
cellbender:remove-background: [epoch 021]  average training loss: 3042.7906
cellbender:remove-background: [epoch 022]  average training loss: 3012.6435
cellbender:remove-background: [epoch 023]  average training loss: 2981.3115
cellbender:remove-background: [epoch 024]  average training loss: 2963.3271
cellbender:remove-background: [epoch 025]  average training loss: 2952.6355
cellbender:remove-background: [epoch 025] average test loss: 2932.8359
cellbender:remove-background: [epoch 026]  average training loss: 2942.6782
cellbender:remove-background: [epoch 027]  average training loss: 2936.9395
cellbender:remove-background: [epoch 028]  average training loss: 2935.2085
cellbender:remove-background: [epoch 029]  average training loss: 2927.4479
cellbender:remove-background: [epoch 030]  average training loss: 2922.9505
cellbender:remove-background: [epoch 030] average test loss: 2884.9017
cellbender:remove-background: [epoch 031]  average training loss: 2918.2425
cellbender:remove-background: [epoch 032]  average training loss: 2911.5287
cellbender:remove-background: [epoch 033]  average training loss: 2909.8984
cellbender:remove-background: [epoch 034]  average training loss: 2905.4729
cellbender:remove-background: [epoch 035]  average training loss: 2903.2492
cellbender:remove-background: [epoch 035] average test loss: 2872.8802
cellbender:remove-background: [epoch 036]  average training loss: 2900.6143
cellbender:remove-background: [epoch 037]  average training loss: 2898.7787
cellbender:remove-background: [epoch 038]  average training loss: 2897.2393
cellbender:remove-background: [epoch 039]  average training loss: 2892.1278
cellbender:remove-background: [epoch 040]  average training loss: 2894.9860
cellbender:remove-background: [epoch 040] average test loss: 2853.9035
cellbender:remove-background: [epoch 041]  average training loss: 2892.3336
cellbender:remove-background: [epoch 042]  average training loss: 2889.2839
cellbender:remove-background: [epoch 043]  average training loss: 2891.2966
cellbender:remove-background: [epoch 044]  average training loss: 2891.6013
cellbender:remove-background: [epoch 045]  average training loss: 2888.4878
cellbender:remove-background: [epoch 045] average test loss: 2846.1657
cellbender:remove-background: [epoch 046]  average training loss: 2891.2564
cellbender:remove-background: [epoch 047]  average training loss: 2890.9071
cellbender:remove-background: [epoch 048]  average training loss: 2891.8815
cellbender:remove-background: [epoch 049]  average training loss: 2894.0800
cellbender:remove-background: [epoch 050]  average training loss: 2889.9986
cellbender:remove-background: [epoch 050] average test loss: 2854.4460
cellbender:remove-background: [epoch 051]  average training loss: 2890.2397
cellbender:remove-background: [epoch 052]  average training loss: 2891.3218
cellbender:remove-background: [epoch 053]  average training loss: 2892.1222
cellbender:remove-background: [epoch 054]  average training loss: 2889.5068
cellbender:remove-background: [epoch 055]  average training loss: 2893.0191
cellbender:remove-background: [epoch 055] average test loss: 2854.4848
cellbender:remove-background: [epoch 056]  average training loss: 2888.6338
cellbender:remove-background: [epoch 057]  average training loss: 2886.1921
cellbender:remove-background: [epoch 058]  average training loss: 2890.2240
cellbender:remove-background: [epoch 059]  average training loss: 2892.7371
cellbender:remove-background: [epoch 060]  average training loss: 2893.4107
cellbender:remove-background: [epoch 060] average test loss: 2863.1802
cellbender:remove-background: [epoch 061]  average training loss: 2892.3948
cellbender:remove-background: [epoch 062]  average training loss: 2890.5984
cellbender:remove-background: [epoch 063]  average training loss: 2895.2636
cellbender:remove-background: [epoch 064]  average training loss: 2893.5151
cellbender:remove-background: [epoch 065]  average training loss: 2892.1801
cellbender:remove-background: [epoch 065] average test loss: 2885.2821
cellbender:remove-background: [epoch 066]  average training loss: 2904.5693
cellbender:remove-background: [epoch 067]  average training loss: 2897.1768
cellbender:remove-background: [epoch 068]  average training loss: 2897.3669
cellbender:remove-background: [epoch 069]  average training loss: 2902.8513
cellbender:remove-background: [epoch 070]  average training loss: 2898.0878
cellbender:remove-background: [epoch 070] average test loss: 2863.2250
cellbender:remove-background: [epoch 071]  average training loss: 2905.9495
cellbender:remove-background: [epoch 072]  average training loss: 2900.2277
cellbender:remove-background: [epoch 073]  average training loss: 2914.6596
cellbender:remove-background: [epoch 074]  average training loss: 2904.2109
cellbender:remove-background: [epoch 075]  average training loss: 2907.5597
cellbender:remove-background: [epoch 075] average test loss: 2903.3229
cellbender:remove-background: [epoch 076]  average training loss: 2902.1021
cellbender:remove-background: [epoch 077]  average training loss: 2899.0364
cellbender:remove-background: [epoch 078]  average training loss: 2896.8644
cellbender:remove-background: [epoch 079]  average training loss: 2905.8095
cellbender:remove-background: [epoch 080]  average training loss: 2908.9848
cellbender:remove-background: [epoch 080] average test loss: 2902.0931
cellbender:remove-background: [epoch 081]  average training loss: 2892.5053
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/1838-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 082]  average training loss: 2917.0574
cellbender:remove-background: [epoch 083]  average training loss: 2904.5221
cellbender:remove-background: [epoch 084]  average training loss: 2904.7264
cellbender:remove-background: [epoch 085]  average training loss: 2892.1826
cellbender:remove-background: [epoch 085] average test loss: 2874.3080
cellbender:remove-background: [epoch 086]  average training loss: 2895.7855
cellbender:remove-background: [epoch 087]  average training loss: 2892.3784
cellbender:remove-background: [epoch 088]  average training loss: 2889.9738
cellbender:remove-background: [epoch 089]  average training loss: 2896.0755
cellbender:remove-background: [epoch 090]  average training loss: 2885.0503
cellbender:remove-background: [epoch 090] average test loss: 2858.1898
cellbender:remove-background: [epoch 091]  average training loss: 2886.0282
cellbender:remove-background: [epoch 092]  average training loss: 2882.3203
cellbender:remove-background: [epoch 093]  average training loss: 2883.6807
cellbender:remove-background: [epoch 094]  average training loss: 2882.9060
cellbender:remove-background: [epoch 095]  average training loss: 2891.3863
cellbender:remove-background: [epoch 095] average test loss: 2901.5563
cellbender:remove-background: [epoch 096]  average training loss: 2878.5280
cellbender:remove-background: [epoch 097]  average training loss: 2885.4295
cellbender:remove-background: [epoch 098]  average training loss: 2886.7303
cellbender:remove-background: [epoch 099]  average training loss: 2885.7742
cellbender:remove-background: [epoch 100]  average training loss: 2880.1855
cellbender:remove-background: [epoch 100] average test loss: 2892.5229
cellbender:remove-background: [epoch 101]  average training loss: 2877.0534
cellbender:remove-background: [epoch 102]  average training loss: 2879.7774
cellbender:remove-background: [epoch 103]  average training loss: 2878.5365
cellbender:remove-background: [epoch 104]  average training loss: 2878.9856
cellbender:remove-background: [epoch 105]  average training loss: 2880.2411
cellbender:remove-background: [epoch 105] average test loss: 2867.8265
cellbender:remove-background: [epoch 106]  average training loss: 2875.7518
cellbender:remove-background: [epoch 107]  average training loss: 2877.8580
cellbender:remove-background: [epoch 108]  average training loss: 2875.3510
cellbender:remove-background: [epoch 109]  average training loss: 2878.6137
cellbender:remove-background: [epoch 110]  average training loss: 2873.1442
cellbender:remove-background: [epoch 110] average test loss: 2868.3886
cellbender:remove-background: [epoch 111]  average training loss: 2877.4423
cellbender:remove-background: [epoch 112]  average training loss: 2872.4855
cellbender:remove-background: [epoch 113]  average training loss: 2874.0985
cellbender:remove-background: [epoch 114]  average training loss: 2878.7767
cellbender:remove-background: [epoch 115]  average training loss: 2874.4760
cellbender:remove-background: [epoch 115] average test loss: 2880.3497
cellbender:remove-background: [epoch 116]  average training loss: 2873.3387
cellbender:remove-background: [epoch 117]  average training loss: 2872.3613
cellbender:remove-background: [epoch 118]  average training loss: 2873.4289
cellbender:remove-background: [epoch 119]  average training loss: 2869.1631
cellbender:remove-background: [epoch 120]  average training loss: 2875.0330
cellbender:remove-background: [epoch 120] average test loss: 2868.2282
cellbender:remove-background: [epoch 121]  average training loss: 2869.2071
cellbender:remove-background: [epoch 122]  average training loss: 2867.4147
cellbender:remove-background: [epoch 123]  average training loss: 2871.8355
cellbender:remove-background: [epoch 124]  average training loss: 2867.5542
cellbender:remove-background: [epoch 125]  average training loss: 2868.5351
cellbender:remove-background: [epoch 125] average test loss: 2870.8559
cellbender:remove-background: [epoch 126]  average training loss: 2869.7617
cellbender:remove-background: [epoch 127]  average training loss: 2868.6859
cellbender:remove-background: [epoch 128]  average training loss: 2865.7235
cellbender:remove-background: [epoch 129]  average training loss: 2870.4261
cellbender:remove-background: [epoch 130]  average training loss: 2867.1525
cellbender:remove-background: [epoch 130] average test loss: 2870.6585
cellbender:remove-background: [epoch 131]  average training loss: 2864.5717
cellbender:remove-background: [epoch 132]  average training loss: 2867.6538
cellbender:remove-background: [epoch 133]  average training loss: 2866.6076
cellbender:remove-background: [epoch 134]  average training loss: 2868.6272
cellbender:remove-background: [epoch 135]  average training loss: 2865.7732
cellbender:remove-background: [epoch 135] average test loss: 2871.1823
cellbender:remove-background: [epoch 136]  average training loss: 2864.5733
cellbender:remove-background: [epoch 137]  average training loss: 2864.1815
cellbender:remove-background: [epoch 138]  average training loss: 2865.8124
cellbender:remove-background: [epoch 139]  average training loss: 2865.2687
cellbender:remove-background: [epoch 140]  average training loss: 2864.2830
cellbender:remove-background: [epoch 140] average test loss: 2875.4577
cellbender:remove-background: [epoch 141]  average training loss: 2865.9837
cellbender:remove-background: [epoch 142]  average training loss: 2864.5076
cellbender:remove-background: [epoch 143]  average training loss: 2864.0927
cellbender:remove-background: [epoch 144]  average training loss: 2864.3055
cellbender:remove-background: [epoch 145]  average training loss: 2866.0770
cellbender:remove-background: [epoch 145] average test loss: 2871.7263
cellbender:remove-background: [epoch 146]  average training loss: 2864.3007
cellbender:remove-background: [epoch 147]  average training loss: 2863.9378
cellbender:remove-background: [epoch 148]  average training loss: 2864.7023
cellbender:remove-background: [epoch 149]  average training loss: 2865.4423
cellbender:remove-background: [epoch 150]  average training loss: 2866.0896
cellbender:remove-background: [epoch 150] average test loss: 2889.6753
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/1838-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:46:36
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpt_iyaiea
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpt_iyaiea
/tmp/tmpt_iyaiea/4ddd6cde6f_random.pyro
/tmp/tmpt_iyaiea/4ddd6cde6f_random.cuda
/tmp/tmpt_iyaiea/4ddd6cde6f_model.torch
/tmp/tmpt_iyaiea/4ddd6cde6f_optim.torch
/tmp/tmpt_iyaiea/4ddd6cde6f_optim.pyro
/tmp/tmpt_iyaiea/4ddd6cde6f_params.pyro
/tmp/tmpt_iyaiea/4ddd6cde6f_train.loaderstate
/tmp/tmpt_iyaiea/4ddd6cde6f_test.loaderstate
/tmp/tmpt_iyaiea/4ddd6cde6f_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 (1/60)
cellbender:remove-background:     [0.03 mins per chunk]
cellbender:remove-background: Working on chunk (2/60)
cellbender:remove-background: Working on chunk (3/60)
cellbender:remove-background: Working on chunk (4/60)
cellbender:remove-background: Working on chunk (5/60)
cellbender:remove-background: Working on chunk (6/60)
cellbender:remove-background: Working on chunk (7/60)
cellbender:remove-background: Working on chunk (8/60)
cellbender:remove-background: Working on chunk (9/60)
cellbender:remove-background: Working on chunk (10/60)
cellbender:remove-background: Working on chunk (11/60)
cellbender:remove-background: Working on chunk (12/60)
cellbender:remove-background: Working on chunk (13/60)
cellbender:remove-background: Working on chunk (14/60)
cellbender:remove-background: Working on chunk (15/60)
cellbender:remove-background: Working on chunk (16/60)
cellbender:remove-background: Working on chunk (17/60)
cellbender:remove-background: Working on chunk (18/60)
cellbender:remove-background: Working on chunk (19/60)
cellbender:remove-background: Working on chunk (20/60)
cellbender:remove-background: Working on chunk (21/60)
cellbender:remove-background: Working on chunk (22/60)
cellbender:remove-background: Working on chunk (23/60)
cellbender:remove-background: Working on chunk (24/60)
cellbender:remove-background: Working on chunk (25/60)
cellbender:remove-background: Working on chunk (26/60)
cellbender:remove-background: Working on chunk (27/60)
cellbender:remove-background: Working on chunk (28/60)
cellbender:remove-background: Working on chunk (29/60)
cellbender:remove-background: Working on chunk (30/60)
cellbender:remove-background: Working on chunk (31/60)
cellbender:remove-background: Working on chunk (32/60)
cellbender:remove-background: Working on chunk (33/60)
cellbender:remove-background: Working on chunk (34/60)
cellbender:remove-background: Working on chunk (35/60)
cellbender:remove-background: Working on chunk (36/60)
cellbender:remove-background: Working on chunk (37/60)
cellbender:remove-background: Working on chunk (38/60)
cellbender:remove-background: Working on chunk (39/60)
cellbender:remove-background: Working on chunk (40/60)
cellbender:remove-background: Working on chunk (41/60)
cellbender:remove-background: Working on chunk (42/60)
cellbender:remove-background: Working on chunk (43/60)
cellbender:remove-background: Working on chunk (44/60)
cellbender:remove-background: Working on chunk (45/60)
cellbender:remove-background: Working on chunk (46/60)
cellbender:remove-background: Working on chunk (47/60)
cellbender:remove-background: Working on chunk (48/60)
cellbender:remove-background: Working on chunk (49/60)
cellbender:remove-background: Working on chunk (50/60)
cellbender:remove-background: Working on chunk (51/60)
cellbender:remove-background: Working on chunk (52/60)
cellbender:remove-background: Working on chunk (53/60)
cellbender:remove-background: Working on chunk (54/60)
cellbender:remove-background: Working on chunk (55/60)
cellbender:remove-background: Working on chunk (56/60)
cellbender:remove-background: Working on chunk (57/60)
cellbender:remove-background: Working on chunk (58/60)
cellbender:remove-background: Working on chunk (59/60)
cellbender:remove-background: Working on chunk (60/60)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1838-Bipolar-DLPFC/1838-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/1838-Bipolar-DLPFC/1838-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:50:03

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1838-Bipolar-DLPFC/1838-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/1838-Bipolar-DLPFC/1838-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:     [1.48 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 16:00:54 Total MCKP estimation time = 623.91 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/1838-Bipolar-DLPFC/1838-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/1838-Bipolar-DLPFC/1838-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/1838-Bipolar-DLPFC/1838-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/1838-Bipolar-DLPFC/1838-Bipolar-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 16:01:12