cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1390-Control-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-dACC/1390-Control-dACC.cellbender.output.h5 --cuda --expected-cells 2854 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 32508580af)
cellbender:remove-background: 2024-06-06 14:54:33
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/1390-Control-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: 31933 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 8041
cellbender:remove-background: Prior on counts for empty droplets is 72
cellbender:remove-background: Excluding 10743 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 21190 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 36
cellbender:remove-background: Using 2854 probable cell barcodes, plus an additional 17146 barcodes, and 58632 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/tmp2nb87mc0
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: 4175.7916
cellbender:remove-background: [epoch 002]  average training loss: 3293.7645  (11.4 seconds per epoch)
cellbender:remove-background: Will checkpoint every 37 epochs
cellbender:remove-background: [epoch 003]  average training loss: 2843.2460
cellbender:remove-background: [epoch 004]  average training loss: 2518.8870
cellbender:remove-background: [epoch 005]  average training loss: 2453.2364
cellbender:remove-background: [epoch 005] average test loss: 2730.8276
cellbender:remove-background: [epoch 006]  average training loss: 2445.2575
cellbender:remove-background: [epoch 007]  average training loss: 2405.3258
cellbender:remove-background: [epoch 008]  average training loss: 2369.7474
cellbender:remove-background: [epoch 009]  average training loss: 2347.3215
cellbender:remove-background: [epoch 010]  average training loss: 2286.8450
cellbender:remove-background: [epoch 010] average test loss: 2325.3266
cellbender:remove-background: [epoch 011]  average training loss: 2261.2615
cellbender:remove-background: [epoch 012]  average training loss: 2228.7706
cellbender:remove-background: [epoch 013]  average training loss: 2186.0195
cellbender:remove-background: [epoch 014]  average training loss: 2160.0320
cellbender:remove-background: [epoch 015]  average training loss: 2115.5441
cellbender:remove-background: [epoch 015] average test loss: 2158.8958
cellbender:remove-background: [epoch 016]  average training loss: 2098.5828
cellbender:remove-background: [epoch 017]  average training loss: 2098.5698
cellbender:remove-background: [epoch 018]  average training loss: 2081.0173
cellbender:remove-background: [epoch 019]  average training loss: 2054.6833
cellbender:remove-background: [epoch 020]  average training loss: 2030.1772
cellbender:remove-background: [epoch 020] average test loss: 2085.6280
cellbender:remove-background: [epoch 021]  average training loss: 2019.0005
cellbender:remove-background: [epoch 022]  average training loss: 2014.8688
cellbender:remove-background: [epoch 023]  average training loss: 2010.1111
cellbender:remove-background: [epoch 024]  average training loss: 1999.6585
cellbender:remove-background: [epoch 025]  average training loss: 1998.6239
cellbender:remove-background: [epoch 025] average test loss: 2045.0012
cellbender:remove-background: [epoch 026]  average training loss: 1989.5831
cellbender:remove-background: [epoch 027]  average training loss: 1987.0991
cellbender:remove-background: [epoch 028]  average training loss: 1984.3596
cellbender:remove-background: [epoch 029]  average training loss: 1981.7528
cellbender:remove-background: [epoch 030]  average training loss: 1976.2027
cellbender:remove-background: [epoch 030] average test loss: 2020.1983
cellbender:remove-background: [epoch 031]  average training loss: 1976.6233
cellbender:remove-background: [epoch 032]  average training loss: 1973.1230
cellbender:remove-background: [epoch 033]  average training loss: 1971.0697
cellbender:remove-background: [epoch 034]  average training loss: 1969.1774
cellbender:remove-background: [epoch 035]  average training loss: 1971.2159
cellbender:remove-background: [epoch 035] average test loss: 2007.4696
cellbender:remove-background: [epoch 036]  average training loss: 1970.0680
cellbender:remove-background: [epoch 037]  average training loss: 1970.3396
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/1390-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 038]  average training loss: 1968.3157
cellbender:remove-background: [epoch 039]  average training loss: 1970.2601
cellbender:remove-background: [epoch 040]  average training loss: 1967.5668
cellbender:remove-background: [epoch 040] average test loss: 2001.2469
cellbender:remove-background: [epoch 041]  average training loss: 1971.2357
cellbender:remove-background: [epoch 042]  average training loss: 1969.7087
cellbender:remove-background: [epoch 043]  average training loss: 1975.1520
cellbender:remove-background: [epoch 044]  average training loss: 1970.7150
cellbender:remove-background: [epoch 045]  average training loss: 1972.5332
cellbender:remove-background: [epoch 045] average test loss: 2011.9786
cellbender:remove-background: [epoch 046]  average training loss: 1972.4845
cellbender:remove-background: [epoch 047]  average training loss: 1974.3758
cellbender:remove-background: [epoch 048]  average training loss: 1974.5372
cellbender:remove-background: [epoch 049]  average training loss: 1976.3768
cellbender:remove-background: [epoch 050]  average training loss: 1978.7782
cellbender:remove-background: [epoch 050] average test loss: 2005.9434
cellbender:remove-background: [epoch 051]  average training loss: 1982.5340
cellbender:remove-background: [epoch 052]  average training loss: 1992.7240
cellbender:remove-background: [epoch 053]  average training loss: 2033.5535
cellbender:remove-background: [epoch 054]  average training loss: 2029.9670
cellbender:remove-background: [epoch 055]  average training loss: 2026.8645
cellbender:remove-background: [epoch 055] average test loss: 2125.9827
cellbender:remove-background: [epoch 056]  average training loss: 2071.2552
cellbender:remove-background: [epoch 057]  average training loss: 2037.5230
cellbender:remove-background: [epoch 058]  average training loss: 2019.1205
cellbender:remove-background: [epoch 059]  average training loss: 2054.7452
cellbender:remove-background: [epoch 060]  average training loss: 2050.5682
cellbender:remove-background: [epoch 060] average test loss: 2122.8234
cellbender:remove-background: [epoch 061]  average training loss: 2048.5521
cellbender:remove-background: [epoch 062]  average training loss: 2048.5470
cellbender:remove-background: [epoch 063]  average training loss: 2077.6948
cellbender:remove-background: [epoch 064]  average training loss: 2064.1763
cellbender:remove-background: [epoch 065]  average training loss: 2096.8963
cellbender:remove-background: [epoch 065] average test loss: 2146.3281
cellbender:remove-background: [epoch 066]  average training loss: 2092.1639
cellbender:remove-background: [epoch 067]  average training loss: 2079.4769
cellbender:remove-background: [epoch 068]  average training loss: 2072.2664
cellbender:remove-background: [epoch 069]  average training loss: 2034.5852
cellbender:remove-background: [epoch 070]  average training loss: 2063.8703
cellbender:remove-background: [epoch 070] average test loss: 2115.5488
cellbender:remove-background: [epoch 071]  average training loss: 2056.7468
cellbender:remove-background: [epoch 072]  average training loss: 2074.8861
cellbender:remove-background: [epoch 073]  average training loss: 2067.4999
cellbender:remove-background: [epoch 074]  average training loss: 2055.2671
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/1390-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 075]  average training loss: 2079.2831
cellbender:remove-background: [epoch 075] average test loss: 2160.3796
cellbender:remove-background: [epoch 076]  average training loss: 2072.0872
cellbender:remove-background: [epoch 077]  average training loss: 2041.5392
cellbender:remove-background: [epoch 078]  average training loss: 2050.2628
cellbender:remove-background: [epoch 079]  average training loss: 2039.0321
cellbender:remove-background: [epoch 080]  average training loss: 2049.1163
cellbender:remove-background: [epoch 080] average test loss: 2174.2578
cellbender:remove-background: [epoch 081]  average training loss: 2065.2456
cellbender:remove-background: [epoch 082]  average training loss: 2059.4351
cellbender:remove-background: [epoch 083]  average training loss: 2066.5714
cellbender:remove-background: [epoch 084]  average training loss: 2072.0482
cellbender:remove-background: [epoch 085]  average training loss: 2064.5291
cellbender:remove-background: [epoch 085] average test loss: 2089.1782
cellbender:remove-background: [epoch 086]  average training loss: 2055.1988
cellbender:remove-background: [epoch 087]  average training loss: 2068.7117
cellbender:remove-background: [epoch 088]  average training loss: 2041.0885
cellbender:remove-background: [epoch 089]  average training loss: 2095.1415
cellbender:remove-background: [epoch 090]  average training loss: 2071.4346
cellbender:remove-background: [epoch 090] average test loss: 2054.0153
cellbender:remove-background: [epoch 091]  average training loss: 2078.1061
cellbender:remove-background: [epoch 092]  average training loss: 2113.1523
cellbender:remove-background: [epoch 093]  average training loss: 2147.2208
cellbender:remove-background: [epoch 094]  average training loss: 2087.5588
cellbender:remove-background: [epoch 095]  average training loss: 2087.7622
cellbender:remove-background: [epoch 095] average test loss: 2184.5588
cellbender:remove-background: [epoch 096]  average training loss: 2062.9332
cellbender:remove-background: [epoch 097]  average training loss: 2137.8972
cellbender:remove-background: [epoch 098]  average training loss: 2091.6706
cellbender:remove-background: [epoch 099]  average training loss: 2109.7411
cellbender:remove-background: [epoch 100]  average training loss: 2081.0067
cellbender:remove-background: [epoch 100] average test loss: 2144.5475
cellbender:remove-background: [epoch 101]  average training loss: 2129.7351
cellbender:remove-background: [epoch 102]  average training loss: 2075.6955
cellbender:remove-background: [epoch 103]  average training loss: 2095.8232
cellbender:remove-background: [epoch 104]  average training loss: 2096.2060
cellbender:remove-background: [epoch 105]  average training loss: 2107.3088
cellbender:remove-background: [epoch 105] average test loss: 2126.2211
cellbender:remove-background: [epoch 106]  average training loss: 2090.6324
cellbender:remove-background: [epoch 107]  average training loss: 2150.8460
cellbender:remove-background: [epoch 108]  average training loss: 2075.9093
cellbender:remove-background: [epoch 109]  average training loss: 2071.9642
cellbender:remove-background: [epoch 110]  average training loss: 2071.1854
cellbender:remove-background: [epoch 110] average test loss: 2185.8336
cellbender:remove-background: [epoch 111]  average training loss: 2126.5511
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/1390-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 112]  average training loss: 2111.1578
cellbender:remove-background: [epoch 113]  average training loss: 2078.3214
cellbender:remove-background: [epoch 114]  average training loss: 2105.5270
cellbender:remove-background: [epoch 115]  average training loss: 2131.4571
cellbender:remove-background: [epoch 115] average test loss: 2110.7113
cellbender:remove-background: [epoch 116]  average training loss: 2105.0884
cellbender:remove-background: [epoch 117]  average training loss: 2100.3210
cellbender:remove-background: [epoch 118]  average training loss: 2074.8961
cellbender:remove-background: [epoch 119]  average training loss: 2079.6691
cellbender:remove-background: [epoch 120]  average training loss: 2106.4893
cellbender:remove-background: [epoch 120] average test loss: 2218.5310
cellbender:remove-background: [epoch 121]  average training loss: 2080.5023
cellbender:remove-background: [epoch 122]  average training loss: 2125.1286
cellbender:remove-background: [epoch 123]  average training loss: 2059.9497
cellbender:remove-background: [epoch 124]  average training loss: 2076.6110
cellbender:remove-background: [epoch 125]  average training loss: 2075.0297
cellbender:remove-background: [epoch 125] average test loss: 2305.7465
cellbender:remove-background: [epoch 126]  average training loss: 2087.0834
cellbender:remove-background: [epoch 127]  average training loss: 2110.1818
cellbender:remove-background: [epoch 128]  average training loss: 2102.0199
cellbender:remove-background: [epoch 129]  average training loss: 2117.7451
cellbender:remove-background: [epoch 130]  average training loss: 2089.9652
cellbender:remove-background: [epoch 130] average test loss: 2170.3413
cellbender:remove-background: [epoch 131]  average training loss: 2066.2911
cellbender:remove-background: [epoch 132]  average training loss: 2066.6708
cellbender:remove-background: [epoch 133]  average training loss: 2078.6830
cellbender:remove-background: [epoch 134]  average training loss: 2076.7258
cellbender:remove-background: [epoch 135]  average training loss: 2108.7696
cellbender:remove-background: [epoch 135] average test loss: 2138.3374
cellbender:remove-background: [epoch 136]  average training loss: 2088.4378
cellbender:remove-background: [epoch 137]  average training loss: 2079.3939
cellbender:remove-background: [epoch 138]  average training loss: 2118.5684
cellbender:remove-background: [epoch 139]  average training loss: 2077.8719
cellbender:remove-background: [epoch 140]  average training loss: 2109.3283
cellbender:remove-background: [epoch 140] average test loss: 2234.3127
cellbender:remove-background: [epoch 141]  average training loss: 2085.4909
cellbender:remove-background: [epoch 142]  average training loss: 2118.9246
cellbender:remove-background: [epoch 143]  average training loss: 2103.8219
cellbender:remove-background: [epoch 144]  average training loss: 2068.5771
cellbender:remove-background: [epoch 145]  average training loss: 2101.6238
cellbender:remove-background: [epoch 145] average test loss: 2365.4073
cellbender:remove-background: [epoch 146]  average training loss: 2098.1171
cellbender:remove-background: [epoch 147]  average training loss: 2085.2098
cellbender:remove-background: [epoch 148]  average training loss: 2104.6571
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/1390-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 149]  average training loss: 2082.9654
cellbender:remove-background: [epoch 150]  average training loss: 2112.5727
cellbender:remove-background: [epoch 150] average test loss: 2197.5615
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/1390-Control-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:31:13
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp_8jtytia
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp_8jtytia
/tmp/tmp_8jtytia/32508580af_random.pyro
/tmp/tmp_8jtytia/32508580af_random.cuda
/tmp/tmp_8jtytia/32508580af_model.torch
/tmp/tmp_8jtytia/32508580af_optim.torch
/tmp/tmp_8jtytia/32508580af_optim.pyro
/tmp/tmp_8jtytia/32508580af_params.pyro
/tmp/tmp_8jtytia/32508580af_train.loaderstate
/tmp/tmp_8jtytia/32508580af_test.loaderstate
/tmp/tmp_8jtytia/32508580af_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 (1/39)
cellbender:remove-background:     [0.06 mins per chunk]
cellbender:remove-background: Working on chunk (2/39)
cellbender:remove-background: Working on chunk (3/39)
cellbender:remove-background: Working on chunk (4/39)
cellbender:remove-background: Working on chunk (5/39)
cellbender:remove-background: Working on chunk (6/39)
cellbender:remove-background: Working on chunk (7/39)
cellbender:remove-background: Working on chunk (8/39)
cellbender:remove-background: Working on chunk (9/39)
cellbender:remove-background: Working on chunk (10/39)
cellbender:remove-background: Working on chunk (11/39)
cellbender:remove-background: Working on chunk (12/39)
cellbender:remove-background: Working on chunk (13/39)
cellbender:remove-background: Working on chunk (14/39)
cellbender:remove-background: Working on chunk (15/39)
cellbender:remove-background: Working on chunk (16/39)
cellbender:remove-background: Working on chunk (17/39)
cellbender:remove-background: Working on chunk (18/39)
cellbender:remove-background: Working on chunk (19/39)
cellbender:remove-background: Working on chunk (20/39)
cellbender:remove-background: Working on chunk (21/39)
cellbender:remove-background: Working on chunk (22/39)
cellbender:remove-background: Working on chunk (23/39)
cellbender:remove-background: Working on chunk (24/39)
cellbender:remove-background: Working on chunk (25/39)
cellbender:remove-background: Working on chunk (26/39)
cellbender:remove-background: Working on chunk (27/39)
cellbender:remove-background: Working on chunk (28/39)
cellbender:remove-background: Working on chunk (29/39)
cellbender:remove-background: Working on chunk (30/39)
cellbender:remove-background: Working on chunk (31/39)
cellbender:remove-background: Working on chunk (32/39)
cellbender:remove-background: Working on chunk (33/39)
cellbender:remove-background: Working on chunk (34/39)
cellbender:remove-background: Working on chunk (35/39)
cellbender:remove-background: Working on chunk (36/39)
cellbender:remove-background: Working on chunk (37/39)
cellbender:remove-background: Working on chunk (38/39)
cellbender:remove-background: Working on chunk (39/39)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-dACC/1390-Control-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/1390-Control-dACC/1390-Control-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:35:24

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-dACC/1390-Control-dACC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-dACC/1390-Control-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:     [1.01 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 15:42:54 Total MCKP estimation time = 423.89 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/1390-Control-dACC/1390-Control-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/1390-Control-dACC/1390-Control-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/1390-Control-dACC/1390-Control-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/1390-Control-dACC/1390-Control-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:43:12