cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2520-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-DLPFC/2520-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 6281 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 9eecdf9487)
cellbender:remove-background: 2024-06-06 14:52:14
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/2520-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: 32001 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 5970
cellbender:remove-background: Prior on counts for empty droplets is 42
cellbender:remove-background: Excluding 12018 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 19983 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 21
cellbender:remove-background: Using 6281 probable cell barcodes, plus an additional 13719 barcodes, and 55165 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 42 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp3cnftan3
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: 7109.2707
cellbender:remove-background: [epoch 002]  average training loss: 5499.0169  (4.8 seconds per epoch)
cellbender:remove-background: Will checkpoint every 87 epochs
cellbender:remove-background: [epoch 003]  average training loss: 4527.3302
cellbender:remove-background: [epoch 004]  average training loss: 3907.0592
cellbender:remove-background: [epoch 005]  average training loss: 3614.2490
cellbender:remove-background: [epoch 005] average test loss: 3605.4826
cellbender:remove-background: [epoch 006]  average training loss: 3409.4012
cellbender:remove-background: [epoch 007]  average training loss: 3225.2007
cellbender:remove-background: [epoch 008]  average training loss: 3117.3462
cellbender:remove-background: [epoch 009]  average training loss: 3092.8075
cellbender:remove-background: [epoch 010]  average training loss: 3047.6037
cellbender:remove-background: [epoch 010] average test loss: 3044.5233
cellbender:remove-background: [epoch 011]  average training loss: 3030.3919
cellbender:remove-background: [epoch 012]  average training loss: 2863.9974
cellbender:remove-background: [epoch 013]  average training loss: 2802.0836
cellbender:remove-background: [epoch 014]  average training loss: 2797.6935
cellbender:remove-background: [epoch 015]  average training loss: 2757.5148
cellbender:remove-background: [epoch 015] average test loss: 2746.8930
cellbender:remove-background: [epoch 016]  average training loss: 2732.2416
cellbender:remove-background: [epoch 017]  average training loss: 2735.6793
cellbender:remove-background: [epoch 018]  average training loss: 2728.0229
cellbender:remove-background: [epoch 019]  average training loss: 2705.3838
cellbender:remove-background: [epoch 020]  average training loss: 2676.2734
cellbender:remove-background: [epoch 020] average test loss: 2697.5434
cellbender:remove-background: [epoch 021]  average training loss: 2662.8336
cellbender:remove-background: [epoch 022]  average training loss: 2650.7437
cellbender:remove-background: [epoch 023]  average training loss: 2635.9263
cellbender:remove-background: [epoch 024]  average training loss: 2617.1746
cellbender:remove-background: [epoch 025]  average training loss: 2614.2452
cellbender:remove-background: [epoch 025] average test loss: 2632.5088
cellbender:remove-background: [epoch 026]  average training loss: 2601.2378
cellbender:remove-background: [epoch 027]  average training loss: 2604.8466
cellbender:remove-background: [epoch 028]  average training loss: 2607.3894
cellbender:remove-background: [epoch 029]  average training loss: 2601.2736
cellbender:remove-background: [epoch 030]  average training loss: 2597.8211
cellbender:remove-background: [epoch 030] average test loss: 2558.2820
cellbender:remove-background: [epoch 031]  average training loss: 2580.5638
cellbender:remove-background: [epoch 032]  average training loss: 2594.8128
cellbender:remove-background: [epoch 033]  average training loss: 2583.4897
cellbender:remove-background: [epoch 034]  average training loss: 2583.0486
cellbender:remove-background: [epoch 035]  average training loss: 2580.2982
cellbender:remove-background: [epoch 035] average test loss: 2588.1486
cellbender:remove-background: [epoch 036]  average training loss: 2608.2259
cellbender:remove-background: [epoch 037]  average training loss: 2609.9207
cellbender:remove-background: [epoch 038]  average training loss: 2596.4102
cellbender:remove-background: [epoch 039]  average training loss: 2619.7626
cellbender:remove-background: [epoch 040]  average training loss: 2652.3898
cellbender:remove-background: [epoch 040] average test loss: 2544.1438
cellbender:remove-background: [epoch 041]  average training loss: 2630.1680
cellbender:remove-background: [epoch 042]  average training loss: 2635.1584
cellbender:remove-background: [epoch 043]  average training loss: 2605.0370
cellbender:remove-background: [epoch 044]  average training loss: 2651.2998
cellbender:remove-background: [epoch 045]  average training loss: 2679.4108
cellbender:remove-background: [epoch 045] average test loss: 2541.5208
cellbender:remove-background: [epoch 046]  average training loss: 2635.5074
cellbender:remove-background: [epoch 047]  average training loss: 2634.0940
cellbender:remove-background: [epoch 048]  average training loss: 2627.1565
cellbender:remove-background: [epoch 049]  average training loss: 2665.8334
cellbender:remove-background: [epoch 050]  average training loss: 2665.7969
cellbender:remove-background: [epoch 050] average test loss: 2669.4354
cellbender:remove-background: [epoch 051]  average training loss: 2670.1796
cellbender:remove-background: [epoch 052]  average training loss: 2578.9498
cellbender:remove-background: [epoch 053]  average training loss: 2601.4768
cellbender:remove-background: [epoch 054]  average training loss: 2623.4259
cellbender:remove-background: [epoch 055]  average training loss: 2650.1488
cellbender:remove-background: [epoch 055] average test loss: 2588.3003
cellbender:remove-background: [epoch 056]  average training loss: 2634.0040
cellbender:remove-background: [epoch 057]  average training loss: 2611.4706
cellbender:remove-background: [epoch 058]  average training loss: 2613.1803
cellbender:remove-background: [epoch 059]  average training loss: 2663.0823
cellbender:remove-background: [epoch 060]  average training loss: 2610.2583
cellbender:remove-background: [epoch 060] average test loss: 2554.3570
cellbender:remove-background: [epoch 061]  average training loss: 2604.8842
cellbender:remove-background: [epoch 062]  average training loss: 2622.8287
cellbender:remove-background: [epoch 063]  average training loss: 2585.6361
cellbender:remove-background: [epoch 064]  average training loss: 2632.6805
cellbender:remove-background: [epoch 065]  average training loss: 2597.7344
cellbender:remove-background: [epoch 065] average test loss: 2545.6768
cellbender:remove-background: [epoch 066]  average training loss: 2587.3358
cellbender:remove-background: [epoch 067]  average training loss: 2593.6937
cellbender:remove-background: [epoch 068]  average training loss: 2597.5142
cellbender:remove-background: [epoch 069]  average training loss: 2587.9793
cellbender:remove-background: [epoch 070]  average training loss: 2625.7803
cellbender:remove-background: [epoch 070] average test loss: 2561.4213
cellbender:remove-background: [epoch 071]  average training loss: 2612.1816
cellbender:remove-background: [epoch 072]  average training loss: 2578.8957
cellbender:remove-background: [epoch 073]  average training loss: 2606.7548
cellbender:remove-background: [epoch 074]  average training loss: 2601.3271
cellbender:remove-background: [epoch 075]  average training loss: 2582.7631
cellbender:remove-background: [epoch 075] average test loss: 2619.0020
cellbender:remove-background: [epoch 076]  average training loss: 2600.8669
cellbender:remove-background: [epoch 077]  average training loss: 2610.7132
cellbender:remove-background: [epoch 078]  average training loss: 2575.1337
cellbender:remove-background: [epoch 079]  average training loss: 2597.7460
cellbender:remove-background: [epoch 080]  average training loss: 2586.5862
cellbender:remove-background: [epoch 080] average test loss: 2582.5056
cellbender:remove-background: [epoch 081]  average training loss: 2571.6126
cellbender:remove-background: [epoch 082]  average training loss: 2578.4005
cellbender:remove-background: [epoch 083]  average training loss: 2583.0117
cellbender:remove-background: [epoch 084]  average training loss: 2602.2461
cellbender:remove-background: [epoch 085]  average training loss: 2629.0390
cellbender:remove-background: [epoch 085] average test loss: 2605.3025
cellbender:remove-background: [epoch 086]  average training loss: 2604.8848
cellbender:remove-background: [epoch 087]  average training loss: 2579.0097
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/2520-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 088]  average training loss: 2594.3301
cellbender:remove-background: [epoch 089]  average training loss: 2567.1553
cellbender:remove-background: [epoch 090]  average training loss: 2598.6051
cellbender:remove-background: [epoch 090] average test loss: 2591.3652
cellbender:remove-background: [epoch 091]  average training loss: 2589.1387
cellbender:remove-background: [epoch 092]  average training loss: 2595.4516
cellbender:remove-background: [epoch 093]  average training loss: 2579.5738
cellbender:remove-background: [epoch 094]  average training loss: 2602.1755
cellbender:remove-background: [epoch 095]  average training loss: 2601.7198
cellbender:remove-background: [epoch 095] average test loss: 2573.0208
cellbender:remove-background: [epoch 096]  average training loss: 2587.2379
cellbender:remove-background: [epoch 097]  average training loss: 2587.7311
cellbender:remove-background: [epoch 098]  average training loss: 2599.6226
cellbender:remove-background: [epoch 099]  average training loss: 2586.8715
cellbender:remove-background: [epoch 100]  average training loss: 2578.6415
cellbender:remove-background: [epoch 100] average test loss: 2566.5223
cellbender:remove-background: [epoch 101]  average training loss: 2585.0915
cellbender:remove-background: [epoch 102]  average training loss: 2594.9148
cellbender:remove-background: [epoch 103]  average training loss: 2596.6839
cellbender:remove-background: [epoch 104]  average training loss: 2583.7909
cellbender:remove-background: [epoch 105]  average training loss: 2578.1308
cellbender:remove-background: [epoch 105] average test loss: 2594.6763
cellbender:remove-background: [epoch 106]  average training loss: 2588.4019
cellbender:remove-background: [epoch 107]  average training loss: 2577.0846
cellbender:remove-background: [epoch 108]  average training loss: 2586.7747
cellbender:remove-background: [epoch 109]  average training loss: 2602.8402
cellbender:remove-background: [epoch 110]  average training loss: 2580.6804
cellbender:remove-background: [epoch 110] average test loss: 2593.7884
cellbender:remove-background: [epoch 111]  average training loss: 2572.7441
cellbender:remove-background: [epoch 112]  average training loss: 2584.2924
cellbender:remove-background: [epoch 113]  average training loss: 2591.6439
cellbender:remove-background: [epoch 114]  average training loss: 2592.4853
cellbender:remove-background: [epoch 115]  average training loss: 2596.2377
cellbender:remove-background: [epoch 115] average test loss: 2579.1323
cellbender:remove-background: [epoch 116]  average training loss: 2573.4753
cellbender:remove-background: [epoch 117]  average training loss: 2600.7560
cellbender:remove-background: [epoch 118]  average training loss: 2577.9350
cellbender:remove-background: [epoch 119]  average training loss: 2569.2725
cellbender:remove-background: [epoch 120]  average training loss: 2578.5300
cellbender:remove-background: [epoch 120] average test loss: 2609.7683
cellbender:remove-background: [epoch 121]  average training loss: 2580.0019
cellbender:remove-background: [epoch 122]  average training loss: 2565.9927
cellbender:remove-background: [epoch 123]  average training loss: 2576.3721
cellbender:remove-background: [epoch 124]  average training loss: 2571.9106
cellbender:remove-background: [epoch 125]  average training loss: 2597.4334
cellbender:remove-background: [epoch 125] average test loss: 2568.9864
cellbender:remove-background: [epoch 126]  average training loss: 2575.0145
cellbender:remove-background: [epoch 127]  average training loss: 2571.2680
cellbender:remove-background: [epoch 128]  average training loss: 2580.0629
cellbender:remove-background: [epoch 129]  average training loss: 2571.8258
cellbender:remove-background: [epoch 130]  average training loss: 2569.0914
cellbender:remove-background: [epoch 130] average test loss: 2576.2034
cellbender:remove-background: [epoch 131]  average training loss: 2563.7625
cellbender:remove-background: [epoch 132]  average training loss: 2562.2941
cellbender:remove-background: [epoch 133]  average training loss: 2571.1538
cellbender:remove-background: [epoch 134]  average training loss: 2571.5294
cellbender:remove-background: [epoch 135]  average training loss: 2560.0987
cellbender:remove-background: [epoch 135] average test loss: 2568.1034
cellbender:remove-background: [epoch 136]  average training loss: 2569.4436
cellbender:remove-background: [epoch 137]  average training loss: 2574.8976
cellbender:remove-background: [epoch 138]  average training loss: 2576.5760
cellbender:remove-background: [epoch 139]  average training loss: 2569.5283
cellbender:remove-background: [epoch 140]  average training loss: 2585.1738
cellbender:remove-background: [epoch 140] average test loss: 2572.0607
cellbender:remove-background: [epoch 141]  average training loss: 2571.3677
cellbender:remove-background: [epoch 142]  average training loss: 2563.6247
cellbender:remove-background: [epoch 143]  average training loss: 2570.6071
cellbender:remove-background: [epoch 144]  average training loss: 2578.3439
cellbender:remove-background: [epoch 145]  average training loss: 2570.0061
cellbender:remove-background: [epoch 145] average test loss: 2589.9764
cellbender:remove-background: [epoch 146]  average training loss: 2566.0766
cellbender:remove-background: [epoch 147]  average training loss: 2569.0101
cellbender:remove-background: [epoch 148]  average training loss: 2568.5945
cellbender:remove-background: [epoch 149]  average training loss: 2568.4617
cellbender:remove-background: [epoch 150]  average training loss: 2572.0533
cellbender:remove-background: [epoch 150] average test loss: 2575.3189
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/2520-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:06:34
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpy59670af
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpy59670af
/tmp/tmpy59670af/9eecdf9487_random.pyro
/tmp/tmpy59670af/9eecdf9487_random.cuda
/tmp/tmpy59670af/9eecdf9487_model.torch
/tmp/tmpy59670af/9eecdf9487_optim.torch
/tmp/tmpy59670af/9eecdf9487_optim.pyro
/tmp/tmpy59670af/9eecdf9487_params.pyro
/tmp/tmpy59670af/9eecdf9487_train.loaderstate
/tmp/tmpy59670af/9eecdf9487_test.loaderstate
/tmp/tmpy59670af/9eecdf9487_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 (1/58)
cellbender:remove-background:     [0.03 mins per chunk]
cellbender:remove-background: Working on chunk (2/58)
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cellbender:remove-background: Working on chunk (51/58)
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cellbender:remove-background: Working on chunk (54/58)
cellbender:remove-background: Working on chunk (55/58)
cellbender:remove-background: Working on chunk (56/58)
cellbender:remove-background: Working on chunk (57/58)
cellbender:remove-background: Working on chunk (58/58)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-DLPFC/2520-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/2520-Bipolar-DLPFC/2520-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:09:44

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2520-Bipolar-DLPFC/2520-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/2520-Bipolar-DLPFC/2520-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:     [1.27 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 15:19:03 Total MCKP estimation time = 534.85 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/2520-Bipolar-DLPFC/2520-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/2520-Bipolar-DLPFC/2520-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/2520-Bipolar-DLPFC/2520-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/2520-Bipolar-DLPFC/2520-Bipolar-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:19:20