cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2927-Control-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2927-Control-DLPFC/2927-Control-DLPFC.cellbender.output.h5 --cuda --expected-cells 4262 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 784b0cf1e4)
cellbender:remove-background: 2024-06-06 15:33:06
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/2927-Control-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: 31322 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 2622
cellbender:remove-background: Prior on counts for empty droplets is 62
cellbender:remove-background: Excluding 10119 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 21203 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 31
cellbender:remove-background: Using 4262 probable cell barcodes, plus an additional 15738 barcodes, and 51996 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 61 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp536tfsfm
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: 3300.9950
cellbender:remove-background: [epoch 002]  average training loss: 2642.9584  (12.2 seconds per epoch)
cellbender:remove-background: Will checkpoint every 35 epochs
cellbender:remove-background: [epoch 003]  average training loss: 2276.3949
cellbender:remove-background: [epoch 004]  average training loss: 2029.5374
cellbender:remove-background: [epoch 005]  average training loss: 1952.5405
cellbender:remove-background: [epoch 005] average test loss: 2155.9653
cellbender:remove-background: [epoch 006]  average training loss: 1926.2654
cellbender:remove-background: [epoch 007]  average training loss: 1902.7295
cellbender:remove-background: [epoch 008]  average training loss: 1881.2637
cellbender:remove-background: [epoch 009]  average training loss: 1871.1474
cellbender:remove-background: [epoch 010]  average training loss: 1854.3658
cellbender:remove-background: [epoch 010] average test loss: 1913.7891
cellbender:remove-background: [epoch 011]  average training loss: 1846.7911
cellbender:remove-background: [epoch 012]  average training loss: 1767.3137
cellbender:remove-background: [epoch 013]  average training loss: 1729.1458
cellbender:remove-background: [epoch 014]  average training loss: 1728.4696
cellbender:remove-background: [epoch 015]  average training loss: 1712.6796
cellbender:remove-background: [epoch 015] average test loss: 1748.3194
cellbender:remove-background: [epoch 016]  average training loss: 1698.9189
cellbender:remove-background: [epoch 017]  average training loss: 1697.7109
cellbender:remove-background: [epoch 018]  average training loss: 1690.5844
cellbender:remove-background: [epoch 019]  average training loss: 1681.1315
cellbender:remove-background: [epoch 020]  average training loss: 1670.0830
cellbender:remove-background: [epoch 020] average test loss: 1724.0929
cellbender:remove-background: [epoch 021]  average training loss: 1676.1213
cellbender:remove-background: [epoch 022]  average training loss: 1674.8978
cellbender:remove-background: [epoch 023]  average training loss: 1673.1942
cellbender:remove-background: [epoch 024]  average training loss: 1667.7933
cellbender:remove-background: [epoch 025]  average training loss: 1665.1548
cellbender:remove-background: [epoch 025] average test loss: 1699.4701
cellbender:remove-background: [epoch 026]  average training loss: 1649.4279
cellbender:remove-background: [epoch 027]  average training loss: 1641.7834
cellbender:remove-background: [epoch 028]  average training loss: 1636.3191
cellbender:remove-background: [epoch 029]  average training loss: 1632.0329
cellbender:remove-background: [epoch 030]  average training loss: 1629.0878
cellbender:remove-background: [epoch 030] average test loss: 1679.5971
cellbender:remove-background: [epoch 031]  average training loss: 1629.8972
cellbender:remove-background: [epoch 032]  average training loss: 1633.4374
cellbender:remove-background: [epoch 033]  average training loss: 1631.7404
cellbender:remove-background: [epoch 034]  average training loss: 1628.4742
cellbender:remove-background: [epoch 035]  average training loss: 1628.4961
cellbender:remove-background: [epoch 035] average test loss: 1675.3864
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/2927-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 036]  average training loss: 1644.1965
cellbender:remove-background: [epoch 037]  average training loss: 1639.8958
cellbender:remove-background: [epoch 038]  average training loss: 1641.7727
cellbender:remove-background: [epoch 039]  average training loss: 1633.6238
cellbender:remove-background: [epoch 040]  average training loss: 1635.9402
cellbender:remove-background: [epoch 040] average test loss: 1676.8841
cellbender:remove-background: [epoch 041]  average training loss: 1656.0769
cellbender:remove-background: [epoch 042]  average training loss: 1649.0507
cellbender:remove-background: [epoch 043]  average training loss: 1654.9103
cellbender:remove-background: [epoch 044]  average training loss: 1641.0834
cellbender:remove-background: [epoch 045]  average training loss: 1649.1473
cellbender:remove-background: [epoch 045] average test loss: 1700.4601
cellbender:remove-background: [epoch 046]  average training loss: 1654.4619
cellbender:remove-background: [epoch 047]  average training loss: 1649.5698
cellbender:remove-background: [epoch 048]  average training loss: 1649.9143
cellbender:remove-background: [epoch 049]  average training loss: 1642.6653
cellbender:remove-background: [epoch 050]  average training loss: 1650.2613
cellbender:remove-background: [epoch 050] average test loss: 1684.5479
cellbender:remove-background: [epoch 051]  average training loss: 1640.8385
cellbender:remove-background: [epoch 052]  average training loss: 1661.7054
cellbender:remove-background: [epoch 053]  average training loss: 1642.2890
cellbender:remove-background: [epoch 054]  average training loss: 1655.5601
cellbender:remove-background: [epoch 055]  average training loss: 1652.2945
cellbender:remove-background: [epoch 055] average test loss: 1698.7290
cellbender:remove-background: [epoch 056]  average training loss: 1647.1084
cellbender:remove-background: [epoch 057]  average training loss: 1655.1810
cellbender:remove-background: [epoch 058]  average training loss: 1656.7414
cellbender:remove-background: [epoch 059]  average training loss: 1635.4484
cellbender:remove-background: [epoch 060]  average training loss: 1637.2986
cellbender:remove-background: [epoch 060] average test loss: 1695.1096
cellbender:remove-background: [epoch 061]  average training loss: 1640.0047
cellbender:remove-background: [epoch 062]  average training loss: 1636.7299
cellbender:remove-background: [epoch 063]  average training loss: 1633.5540
cellbender:remove-background: [epoch 064]  average training loss: 1651.2275
cellbender:remove-background: [epoch 065]  average training loss: 1655.6115
cellbender:remove-background: [epoch 065] average test loss: 1700.9643
cellbender:remove-background: [epoch 066]  average training loss: 1636.2729
cellbender:remove-background: [epoch 067]  average training loss: 1647.8093
cellbender:remove-background: [epoch 068]  average training loss: 1642.2891
cellbender:remove-background: [epoch 069]  average training loss: 1635.5855
cellbender:remove-background: [epoch 070]  average training loss: 1635.1781
cellbender:remove-background: [epoch 070] average test loss: 1711.4483
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/2927-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 071]  average training loss: 1630.6167
cellbender:remove-background: [epoch 072]  average training loss: 1637.3990
cellbender:remove-background: [epoch 073]  average training loss: 1631.4133
cellbender:remove-background: [epoch 074]  average training loss: 1638.9410
cellbender:remove-background: [epoch 075]  average training loss: 1641.0545
cellbender:remove-background: [epoch 075] average test loss: 1702.3142
cellbender:remove-background: [epoch 076]  average training loss: 1637.0962
cellbender:remove-background: [epoch 077]  average training loss: 1637.3470
cellbender:remove-background: [epoch 078]  average training loss: 1632.9780
cellbender:remove-background: [epoch 079]  average training loss: 1633.9511
cellbender:remove-background: [epoch 080]  average training loss: 1636.5639
cellbender:remove-background: [epoch 080] average test loss: 1725.7813
cellbender:remove-background: [epoch 081]  average training loss: 1638.7766
cellbender:remove-background: [epoch 082]  average training loss: 1639.9042
cellbender:remove-background: [epoch 083]  average training loss: 1645.0900
cellbender:remove-background: [epoch 084]  average training loss: 1646.6712
cellbender:remove-background: [epoch 085]  average training loss: 1641.6022
cellbender:remove-background: [epoch 085] average test loss: 1700.1991
cellbender:remove-background: [epoch 086]  average training loss: 1647.1392
cellbender:remove-background: [epoch 087]  average training loss: 1641.6429
cellbender:remove-background: [epoch 088]  average training loss: 1638.4596
cellbender:remove-background: [epoch 089]  average training loss: 1649.9159
cellbender:remove-background: [epoch 090]  average training loss: 1642.4722
cellbender:remove-background: [epoch 090] average test loss: 1720.3938
cellbender:remove-background: [epoch 091]  average training loss: 1647.9470
cellbender:remove-background: [epoch 092]  average training loss: 1643.8612
cellbender:remove-background: [epoch 093]  average training loss: 1641.3746
cellbender:remove-background: [epoch 094]  average training loss: 1648.5220
cellbender:remove-background: [epoch 095]  average training loss: 1660.3988
cellbender:remove-background: [epoch 095] average test loss: 1700.7375
cellbender:remove-background: [epoch 096]  average training loss: 1641.2966
cellbender:remove-background: [epoch 097]  average training loss: 1636.5157
cellbender:remove-background: [epoch 098]  average training loss: 1639.9469
cellbender:remove-background: [epoch 099]  average training loss: 1645.6528
cellbender:remove-background: [epoch 100]  average training loss: 1638.8773
cellbender:remove-background: [epoch 100] average test loss: 1720.7811
cellbender:remove-background: [epoch 101]  average training loss: 1644.3785
cellbender:remove-background: [epoch 102]  average training loss: 1642.9888
cellbender:remove-background: [epoch 103]  average training loss: 1637.6906
cellbender:remove-background: [epoch 104]  average training loss: 1638.9340
cellbender:remove-background: [epoch 105]  average training loss: 1644.8214
cellbender:remove-background: [epoch 105] average test loss: 1705.1289
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/2927-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 106]  average training loss: 1638.4957
cellbender:remove-background: [epoch 107]  average training loss: 1647.2961
cellbender:remove-background: [epoch 108]  average training loss: 1644.7212
cellbender:remove-background: [epoch 109]  average training loss: 1641.3869
cellbender:remove-background: [epoch 110]  average training loss: 1640.9651
cellbender:remove-background: [epoch 110] average test loss: 1728.0225
cellbender:remove-background: [epoch 111]  average training loss: 1645.9802
cellbender:remove-background: [epoch 112]  average training loss: 1640.2117
cellbender:remove-background: [epoch 113]  average training loss: 1642.8134
cellbender:remove-background: [epoch 114]  average training loss: 1636.2873
cellbender:remove-background: [epoch 115]  average training loss: 1643.2773
cellbender:remove-background: [epoch 115] average test loss: 1721.9729
cellbender:remove-background: [epoch 116]  average training loss: 1635.0100
cellbender:remove-background: [epoch 117]  average training loss: 1642.4481
cellbender:remove-background: [epoch 118]  average training loss: 1639.3464
cellbender:remove-background: [epoch 119]  average training loss: 1632.7434
cellbender:remove-background: [epoch 120]  average training loss: 1638.8695
cellbender:remove-background: [epoch 120] average test loss: 1707.6115
cellbender:remove-background: [epoch 121]  average training loss: 1636.2403
cellbender:remove-background: [epoch 122]  average training loss: 1636.3681
cellbender:remove-background: [epoch 123]  average training loss: 1641.4776
cellbender:remove-background: [epoch 124]  average training loss: 1634.4383
cellbender:remove-background: [epoch 125]  average training loss: 1635.5168
cellbender:remove-background: [epoch 125] average test loss: 1712.6803
cellbender:remove-background: [epoch 126]  average training loss: 1633.0062
cellbender:remove-background: [epoch 127]  average training loss: 1630.3220
cellbender:remove-background: [epoch 128]  average training loss: 1630.7336
cellbender:remove-background: [epoch 129]  average training loss: 1633.9497
cellbender:remove-background: [epoch 130]  average training loss: 1634.3072
cellbender:remove-background: [epoch 130] average test loss: 1700.2724
cellbender:remove-background: [epoch 131]  average training loss: 1632.4988
cellbender:remove-background: [epoch 132]  average training loss: 1637.4996
cellbender:remove-background: [epoch 133]  average training loss: 1635.8992
cellbender:remove-background: [epoch 134]  average training loss: 1634.0850
cellbender:remove-background: [epoch 135]  average training loss: 1635.1675
cellbender:remove-background: [epoch 135] average test loss: 1710.5481
cellbender:remove-background: [epoch 136]  average training loss: 1635.8346
cellbender:remove-background: [epoch 137]  average training loss: 1630.2295
cellbender:remove-background: [epoch 138]  average training loss: 1633.7595
cellbender:remove-background: [epoch 139]  average training loss: 1634.5981
cellbender:remove-background: [epoch 140]  average training loss: 1632.4216
cellbender:remove-background: [epoch 140] average test loss: 1713.8689
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/2927-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 141]  average training loss: 1633.3136
cellbender:remove-background: [epoch 142]  average training loss: 1637.1705
cellbender:remove-background: [epoch 143]  average training loss: 1633.3845
cellbender:remove-background: [epoch 144]  average training loss: 1631.9073
cellbender:remove-background: [epoch 145]  average training loss: 1633.0699
cellbender:remove-background: [epoch 145] average test loss: 1706.0395
cellbender:remove-background: [epoch 146]  average training loss: 1631.7338
cellbender:remove-background: [epoch 147]  average training loss: 1636.6031
cellbender:remove-background: [epoch 148]  average training loss: 1635.6293
cellbender:remove-background: [epoch 149]  average training loss: 1633.2409
cellbender:remove-background: [epoch 150]  average training loss: 1632.8067
cellbender:remove-background: [epoch 150] average test loss: 1714.4318
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/2927-Control-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 16:10:42
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpnavd5to7
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpnavd5to7
/tmp/tmpnavd5to7/784b0cf1e4_random.pyro
/tmp/tmpnavd5to7/784b0cf1e4_random.cuda
/tmp/tmpnavd5to7/784b0cf1e4_model.torch
/tmp/tmpnavd5to7/784b0cf1e4_optim.torch
/tmp/tmpnavd5to7/784b0cf1e4_optim.pyro
/tmp/tmpnavd5to7/784b0cf1e4_params.pyro
/tmp/tmpnavd5to7/784b0cf1e4_train.loaderstate
/tmp/tmpnavd5to7/784b0cf1e4_test.loaderstate
/tmp/tmpnavd5to7/784b0cf1e4_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 (1/43)
cellbender:remove-background:     [0.06 mins per chunk]
cellbender:remove-background: Working on chunk (2/43)
cellbender:remove-background: Working on chunk (3/43)
cellbender:remove-background: Working on chunk (4/43)
cellbender:remove-background: Working on chunk (5/43)
cellbender:remove-background: Working on chunk (6/43)
cellbender:remove-background: Working on chunk (7/43)
cellbender:remove-background: Working on chunk (8/43)
cellbender:remove-background: Working on chunk (9/43)
cellbender:remove-background: Working on chunk (10/43)
cellbender:remove-background: Working on chunk (11/43)
cellbender:remove-background: Working on chunk (12/43)
cellbender:remove-background: Working on chunk (13/43)
cellbender:remove-background: Working on chunk (14/43)
cellbender:remove-background: Working on chunk (15/43)
cellbender:remove-background: Working on chunk (16/43)
cellbender:remove-background: Working on chunk (17/43)
cellbender:remove-background: Working on chunk (18/43)
cellbender:remove-background: Working on chunk (19/43)
cellbender:remove-background: Working on chunk (20/43)
cellbender:remove-background: Working on chunk (21/43)
cellbender:remove-background: Working on chunk (22/43)
cellbender:remove-background: Working on chunk (23/43)
cellbender:remove-background: Working on chunk (24/43)
cellbender:remove-background: Working on chunk (25/43)
cellbender:remove-background: Working on chunk (26/43)
cellbender:remove-background: Working on chunk (27/43)
cellbender:remove-background: Working on chunk (28/43)
cellbender:remove-background: Working on chunk (29/43)
cellbender:remove-background: Working on chunk (30/43)
cellbender:remove-background: Working on chunk (31/43)
cellbender:remove-background: Working on chunk (32/43)
cellbender:remove-background: Working on chunk (33/43)
cellbender:remove-background: Working on chunk (34/43)
cellbender:remove-background: Working on chunk (35/43)
cellbender:remove-background: Working on chunk (36/43)
cellbender:remove-background: Working on chunk (37/43)
cellbender:remove-background: Working on chunk (38/43)
cellbender:remove-background: Working on chunk (39/43)
cellbender:remove-background: Working on chunk (40/43)
cellbender:remove-background: Working on chunk (41/43)
cellbender:remove-background: Working on chunk (42/43)
cellbender:remove-background: Working on chunk (43/43)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2927-Control-DLPFC/2927-Control-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/2927-Control-DLPFC/2927-Control-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 16:14:59

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2927-Control-DLPFC/2927-Control-DLPFC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2927-Control-DLPFC/2927-Control-DLPFC.cellbender.output_cell_barcodes.csv
cellbender:remove-background: Computing target noise counts per gene for MCKP estimator
cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01
cellbender:remove-background: Computing denoised counts using mckp estimator
cellbender:remove-background: Working on chunk (1/7)
cellbender:remove-background:     [0.90 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 16:21:34 Total MCKP estimation time = 373.63 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/2927-Control-DLPFC/2927-Control-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/2927-Control-DLPFC/2927-Control-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/2927-Control-DLPFC/2927-Control-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/2927-Control-DLPFC/2927-Control-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 16:21:54