cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1390-Control-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-DLPFC/1390-Control-DLPFC.cellbender.output.h5 --cuda --expected-cells 7128 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash a6454e6595)
cellbender:remove-background: 2024-06-06 14:54:08
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-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: 31189 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 3880
cellbender:remove-background: Prior on counts for empty droplets is 27
cellbender:remove-background: Excluding 11787 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 19402 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 13
cellbender:remove-background: Using 7128 probable cell barcodes, plus an additional 12872 barcodes, and 22231 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 27 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpn5jhxj3d
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: 4502.8925
cellbender:remove-background: [epoch 002]  average training loss: 3593.8974  (5.9 seconds per epoch)
cellbender:remove-background: Will checkpoint every 72 epochs
cellbender:remove-background: [epoch 003]  average training loss: 3123.3914
cellbender:remove-background: [epoch 004]  average training loss: 2863.2510
cellbender:remove-background: [epoch 005]  average training loss: 2791.1403
cellbender:remove-background: [epoch 005] average test loss: 2786.0395
cellbender:remove-background: [epoch 006]  average training loss: 2768.0511
cellbender:remove-background: [epoch 007]  average training loss: 2739.6617
cellbender:remove-background: [epoch 008]  average training loss: 2723.2317
cellbender:remove-background: [epoch 009]  average training loss: 2717.9875
cellbender:remove-background: [epoch 010]  average training loss: 2694.0751
cellbender:remove-background: [epoch 010] average test loss: 2682.1230
cellbender:remove-background: [epoch 011]  average training loss: 2685.9374
cellbender:remove-background: [epoch 012]  average training loss: 2588.4208
cellbender:remove-background: [epoch 013]  average training loss: 2540.1385
cellbender:remove-background: [epoch 014]  average training loss: 2534.5835
cellbender:remove-background: [epoch 015]  average training loss: 2509.1435
cellbender:remove-background: [epoch 015] average test loss: 2502.3210
cellbender:remove-background: [epoch 016]  average training loss: 2492.9546
cellbender:remove-background: [epoch 017]  average training loss: 2491.9117
cellbender:remove-background: [epoch 018]  average training loss: 2483.0739
cellbender:remove-background: [epoch 019]  average training loss: 2473.4494
cellbender:remove-background: [epoch 020]  average training loss: 2462.1454
cellbender:remove-background: [epoch 020] average test loss: 2457.6594
cellbender:remove-background: [epoch 021]  average training loss: 2453.4389
cellbender:remove-background: [epoch 022]  average training loss: 2438.0728
cellbender:remove-background: [epoch 023]  average training loss: 2420.1104
cellbender:remove-background: [epoch 024]  average training loss: 2405.6472
cellbender:remove-background: [epoch 025]  average training loss: 2397.1769
cellbender:remove-background: [epoch 025] average test loss: 2374.9417
cellbender:remove-background: [epoch 026]  average training loss: 2388.5649
cellbender:remove-background: [epoch 027]  average training loss: 2382.5223
cellbender:remove-background: [epoch 028]  average training loss: 2378.1079
cellbender:remove-background: [epoch 029]  average training loss: 2373.0622
cellbender:remove-background: [epoch 030]  average training loss: 2368.6056
cellbender:remove-background: [epoch 030] average test loss: 2339.4810
cellbender:remove-background: [epoch 031]  average training loss: 2364.3493
cellbender:remove-background: [epoch 032]  average training loss: 2361.7645
cellbender:remove-background: [epoch 033]  average training loss: 2362.0399
cellbender:remove-background: [epoch 034]  average training loss: 2358.3753
cellbender:remove-background: [epoch 035]  average training loss: 2356.6230
cellbender:remove-background: [epoch 035] average test loss: 2337.9397
cellbender:remove-background: [epoch 036]  average training loss: 2357.4649
cellbender:remove-background: [epoch 037]  average training loss: 2353.8460
cellbender:remove-background: [epoch 038]  average training loss: 2353.9086
cellbender:remove-background: [epoch 039]  average training loss: 2350.9586
cellbender:remove-background: [epoch 040]  average training loss: 2352.6290
cellbender:remove-background: [epoch 040] average test loss: 2324.0091
cellbender:remove-background: [epoch 041]  average training loss: 2348.1322
cellbender:remove-background: [epoch 042]  average training loss: 2346.6218
cellbender:remove-background: [epoch 043]  average training loss: 2345.3626
cellbender:remove-background: [epoch 044]  average training loss: 2342.2673
cellbender:remove-background: [epoch 045]  average training loss: 2347.1121
cellbender:remove-background: [epoch 045] average test loss: 2318.6306
cellbender:remove-background: [epoch 046]  average training loss: 2343.8186
cellbender:remove-background: [epoch 047]  average training loss: 2341.6317
cellbender:remove-background: [epoch 048]  average training loss: 2338.3895
cellbender:remove-background: [epoch 049]  average training loss: 2343.5768
cellbender:remove-background: [epoch 050]  average training loss: 2338.5574
cellbender:remove-background: [epoch 050] average test loss: 2320.6120
cellbender:remove-background: [epoch 051]  average training loss: 2338.6837
cellbender:remove-background: [epoch 052]  average training loss: 2337.6088
cellbender:remove-background: [epoch 053]  average training loss: 2336.7221
cellbender:remove-background: [epoch 054]  average training loss: 2336.7223
cellbender:remove-background: [epoch 055]  average training loss: 2339.6109
cellbender:remove-background: [epoch 055] average test loss: 2303.4418
cellbender:remove-background: [epoch 056]  average training loss: 2332.5679
cellbender:remove-background: [epoch 057]  average training loss: 2336.0130
cellbender:remove-background: [epoch 058]  average training loss: 2332.8285
cellbender:remove-background: [epoch 059]  average training loss: 2332.8590
cellbender:remove-background: [epoch 060]  average training loss: 2333.7168
cellbender:remove-background: [epoch 060] average test loss: 2319.1121
cellbender:remove-background: [epoch 061]  average training loss: 2334.0009
cellbender:remove-background: [epoch 062]  average training loss: 2331.7034
cellbender:remove-background: [epoch 063]  average training loss: 2329.6779
cellbender:remove-background: [epoch 064]  average training loss: 2332.2077
cellbender:remove-background: [epoch 065]  average training loss: 2330.7177
cellbender:remove-background: [epoch 065] average test loss: 2328.6942
cellbender:remove-background: [epoch 066]  average training loss: 2331.5159
cellbender:remove-background: [epoch 067]  average training loss: 2331.2531
cellbender:remove-background: [epoch 068]  average training loss: 2328.6549
cellbender:remove-background: [epoch 069]  average training loss: 2330.7819
cellbender:remove-background: [epoch 070]  average training loss: 2330.1868
cellbender:remove-background: [epoch 070] average test loss: 2304.5141
cellbender:remove-background: [epoch 071]  average training loss: 2330.4700
cellbender:remove-background: [epoch 072]  average training loss: 2331.0409
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-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 073]  average training loss: 2330.3783
cellbender:remove-background: [epoch 074]  average training loss: 2329.5865
cellbender:remove-background: [epoch 075]  average training loss: 2331.8104
cellbender:remove-background: [epoch 075] average test loss: 2309.0245
cellbender:remove-background: [epoch 076]  average training loss: 2327.8796
cellbender:remove-background: [epoch 077]  average training loss: 2327.3301
cellbender:remove-background: [epoch 078]  average training loss: 2328.0509
cellbender:remove-background: [epoch 079]  average training loss: 2328.7915
cellbender:remove-background: [epoch 080]  average training loss: 2329.8692
cellbender:remove-background: [epoch 080] average test loss: 2305.3953
cellbender:remove-background: [epoch 081]  average training loss: 2326.8944
cellbender:remove-background: [epoch 082]  average training loss: 2327.3137
cellbender:remove-background: [epoch 083]  average training loss: 2327.5164
cellbender:remove-background: [epoch 084]  average training loss: 2327.5437
cellbender:remove-background: [epoch 085]  average training loss: 2327.3975
cellbender:remove-background: [epoch 085] average test loss: 2316.4035
cellbender:remove-background: [epoch 086]  average training loss: 2325.2692
cellbender:remove-background: [epoch 087]  average training loss: 2325.1226
cellbender:remove-background: [epoch 088]  average training loss: 2325.1024
cellbender:remove-background: [epoch 089]  average training loss: 2327.4387
cellbender:remove-background: [epoch 090]  average training loss: 2325.5724
cellbender:remove-background: [epoch 090] average test loss: 2316.3448
cellbender:remove-background: [epoch 091]  average training loss: 2324.5763
cellbender:remove-background: [epoch 092]  average training loss: 2326.6019
cellbender:remove-background: [epoch 093]  average training loss: 2325.9959
cellbender:remove-background: [epoch 094]  average training loss: 2326.9119
cellbender:remove-background: [epoch 095]  average training loss: 2325.6871
cellbender:remove-background: [epoch 095] average test loss: 2327.2255
cellbender:remove-background: [epoch 096]  average training loss: 2324.6790
cellbender:remove-background: [epoch 097]  average training loss: 2325.8988
cellbender:remove-background: [epoch 098]  average training loss: 2325.8736
cellbender:remove-background: [epoch 099]  average training loss: 2325.5171
cellbender:remove-background: [epoch 100]  average training loss: 2324.6758
cellbender:remove-background: [epoch 100] average test loss: 2306.9620
cellbender:remove-background: [epoch 101]  average training loss: 2323.7259
cellbender:remove-background: [epoch 102]  average training loss: 2324.8691
cellbender:remove-background: [epoch 103]  average training loss: 2325.0160
cellbender:remove-background: [epoch 104]  average training loss: 2323.1054
cellbender:remove-background: [epoch 105]  average training loss: 2325.2202
cellbender:remove-background: [epoch 105] average test loss: 2310.0722
cellbender:remove-background: [epoch 106]  average training loss: 2322.2081
cellbender:remove-background: [epoch 107]  average training loss: 2323.2135
cellbender:remove-background: [epoch 108]  average training loss: 2324.3123
cellbender:remove-background: [epoch 109]  average training loss: 2322.2796
cellbender:remove-background: [epoch 110]  average training loss: 2323.8167
cellbender:remove-background: [epoch 110] average test loss: 2330.0881
cellbender:remove-background: [epoch 111]  average training loss: 2327.2810
cellbender:remove-background: [epoch 112]  average training loss: 2323.5708
cellbender:remove-background: [epoch 113]  average training loss: 2325.8545
cellbender:remove-background: [epoch 114]  average training loss: 2319.9515
cellbender:remove-background: [epoch 115]  average training loss: 2324.1236
cellbender:remove-background: [epoch 115] average test loss: 2328.4611
cellbender:remove-background: [epoch 116]  average training loss: 2328.2877
cellbender:remove-background: [epoch 117]  average training loss: 2324.7643
cellbender:remove-background: [epoch 118]  average training loss: 2328.1315
cellbender:remove-background: [epoch 119]  average training loss: 2326.3894
cellbender:remove-background: [epoch 120]  average training loss: 2322.4927
cellbender:remove-background: [epoch 120] average test loss: 2325.6340
cellbender:remove-background: [epoch 121]  average training loss: 2325.9813
cellbender:remove-background: [epoch 122]  average training loss: 2324.9723
cellbender:remove-background: [epoch 123]  average training loss: 2323.1871
cellbender:remove-background: [epoch 124]  average training loss: 2323.8530
cellbender:remove-background: [epoch 125]  average training loss: 2323.6464
cellbender:remove-background: [epoch 125] average test loss: 2324.0166
cellbender:remove-background: [epoch 126]  average training loss: 2323.9851
cellbender:remove-background: [epoch 127]  average training loss: 2322.3247
cellbender:remove-background: [epoch 128]  average training loss: 2323.9736
cellbender:remove-background: [epoch 129]  average training loss: 2324.4300
cellbender:remove-background: [epoch 130]  average training loss: 2323.8369
cellbender:remove-background: [epoch 130] average test loss: 2330.7042
cellbender:remove-background: [epoch 131]  average training loss: 2325.0981
cellbender:remove-background: [epoch 132]  average training loss: 2322.8822
cellbender:remove-background: [epoch 133]  average training loss: 2322.7316
cellbender:remove-background: [epoch 134]  average training loss: 2322.2427
cellbender:remove-background: [epoch 135]  average training loss: 2320.6084
cellbender:remove-background: [epoch 135] average test loss: 2345.1064
cellbender:remove-background: [epoch 136]  average training loss: 2325.4075
cellbender:remove-background: [epoch 137]  average training loss: 2324.0453
cellbender:remove-background: [epoch 138]  average training loss: 2323.4606
cellbender:remove-background: [epoch 139]  average training loss: 2322.0360
cellbender:remove-background: [epoch 140]  average training loss: 2323.7693
cellbender:remove-background: [epoch 140] average test loss: 2329.7327
cellbender:remove-background: [epoch 141]  average training loss: 2322.5943
cellbender:remove-background: [epoch 142]  average training loss: 2321.7422
cellbender:remove-background: [epoch 143]  average training loss: 2321.0276
cellbender:remove-background: [epoch 144]  average training loss: 2323.8945
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-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 145]  average training loss: 2324.7111
cellbender:remove-background: [epoch 145] average test loss: 2328.7187
cellbender:remove-background: [epoch 146]  average training loss: 2320.7542
cellbender:remove-background: [epoch 147]  average training loss: 2324.4416
cellbender:remove-background: [epoch 148]  average training loss: 2322.3757
cellbender:remove-background: [epoch 149]  average training loss: 2321.6758
cellbender:remove-background: [epoch 150]  average training loss: 2322.0309
cellbender:remove-background: [epoch 150] average test loss: 2329.6611
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-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:11:55
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp5n81ygrg
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp5n81ygrg
/tmp/tmp5n81ygrg/a6454e6595_random.pyro
/tmp/tmp5n81ygrg/a6454e6595_random.cuda
/tmp/tmp5n81ygrg/a6454e6595_model.torch
/tmp/tmp5n81ygrg/a6454e6595_optim.torch
/tmp/tmp5n81ygrg/a6454e6595_optim.pyro
/tmp/tmp5n81ygrg/a6454e6595_params.pyro
/tmp/tmp5n81ygrg/a6454e6595_train.loaderstate
/tmp/tmp5n81ygrg/a6454e6595_test.loaderstate
/tmp/tmp5n81ygrg/a6454e6595_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 (1/77)
cellbender:remove-background:     [0.03 mins per chunk]
cellbender:remove-background: Working on chunk (2/77)
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cellbender:remove-background: Working on chunk (77/77)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-DLPFC/1390-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/1390-Control-DLPFC/1390-Control-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:15:41

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1390-Control-DLPFC/1390-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/1390-Control-DLPFC/1390-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:     [1.16 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)
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cellbender:remove-background: Working on chunk (7/7)
cellbender:remove-background: 2024-06-06 15:24:25 Total MCKP estimation time = 478.55 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-DLPFC/1390-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/1390-Control-DLPFC/1390-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/1390-Control-DLPFC/1390-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/1390-Control-DLPFC/1390-Control-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:24:41