cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2673-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2673-Bipolar-DLPFC/2673-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 4346 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash eb932317f5)
cellbender:remove-background: 2024-06-06 15:11:41
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/2673-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: 32053 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 6032
cellbender:remove-background: Prior on counts for empty droplets is 65
cellbender:remove-background: Excluding 10974 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 21079 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 32
cellbender:remove-background: Using 4346 probable cell barcodes, plus an additional 15654 barcodes, and 52318 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 64 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp1hxcqna2
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: 5145.0128
cellbender:remove-background: [epoch 002]  average training loss: 3880.5263  (6.1 seconds per epoch)
cellbender:remove-background: Will checkpoint every 70 epochs
cellbender:remove-background: [epoch 003]  average training loss: 3314.6174
cellbender:remove-background: [epoch 004]  average training loss: 2940.5779
cellbender:remove-background: [epoch 005]  average training loss: 2839.2959
cellbender:remove-background: [epoch 005] average test loss: 3010.4502
cellbender:remove-background: [epoch 006]  average training loss: 2823.0363
cellbender:remove-background: [epoch 007]  average training loss: 2777.0422
cellbender:remove-background: [epoch 008]  average training loss: 2739.1408
cellbender:remove-background: [epoch 009]  average training loss: 2720.1756
cellbender:remove-background: [epoch 010]  average training loss: 2636.7601
cellbender:remove-background: [epoch 010] average test loss: 2647.8032
cellbender:remove-background: [epoch 011]  average training loss: 2555.1925
cellbender:remove-background: [epoch 012]  average training loss: 2522.6674
cellbender:remove-background: [epoch 013]  average training loss: 2493.2738
cellbender:remove-background: [epoch 014]  average training loss: 2509.0131
cellbender:remove-background: [epoch 015]  average training loss: 2472.4301
cellbender:remove-background: [epoch 015] average test loss: 2504.1332
cellbender:remove-background: [epoch 016]  average training loss: 2456.2981
cellbender:remove-background: [epoch 017]  average training loss: 2458.0639
cellbender:remove-background: [epoch 018]  average training loss: 2445.5975
cellbender:remove-background: [epoch 019]  average training loss: 2431.3979
cellbender:remove-background: [epoch 020]  average training loss: 2415.2149
cellbender:remove-background: [epoch 020] average test loss: 2451.2498
cellbender:remove-background: [epoch 021]  average training loss: 2401.8927
cellbender:remove-background: [epoch 022]  average training loss: 2389.3380
cellbender:remove-background: [epoch 023]  average training loss: 2373.4145
cellbender:remove-background: [epoch 024]  average training loss: 2355.9444
cellbender:remove-background: [epoch 025]  average training loss: 2352.1875
cellbender:remove-background: [epoch 025] average test loss: 2381.3356
cellbender:remove-background: [epoch 026]  average training loss: 2337.0466
cellbender:remove-background: [epoch 027]  average training loss: 2331.5085
cellbender:remove-background: [epoch 028]  average training loss: 2330.3915
cellbender:remove-background: [epoch 029]  average training loss: 2323.5621
cellbender:remove-background: [epoch 030]  average training loss: 2321.2497
cellbender:remove-background: [epoch 030] average test loss: 2330.8940
cellbender:remove-background: [epoch 031]  average training loss: 2316.3364
cellbender:remove-background: [epoch 032]  average training loss: 2316.6333
cellbender:remove-background: [epoch 033]  average training loss: 2315.3025
cellbender:remove-background: [epoch 034]  average training loss: 2311.9678
cellbender:remove-background: [epoch 035]  average training loss: 2309.6340
cellbender:remove-background: [epoch 035] average test loss: 2318.9909
cellbender:remove-background: [epoch 036]  average training loss: 2308.9031
cellbender:remove-background: [epoch 037]  average training loss: 2307.3492
cellbender:remove-background: [epoch 038]  average training loss: 2307.1407
cellbender:remove-background: [epoch 039]  average training loss: 2303.9848
cellbender:remove-background: [epoch 040]  average training loss: 2302.7005
cellbender:remove-background: [epoch 040] average test loss: 2324.7493
cellbender:remove-background: [epoch 041]  average training loss: 2303.9744
cellbender:remove-background: [epoch 042]  average training loss: 2301.9179
cellbender:remove-background: [epoch 043]  average training loss: 2304.5636
cellbender:remove-background: [epoch 044]  average training loss: 2301.3785
cellbender:remove-background: [epoch 045]  average training loss: 2301.9137
cellbender:remove-background: [epoch 045] average test loss: 2313.3531
cellbender:remove-background: [epoch 046]  average training loss: 2312.3365
cellbender:remove-background: [epoch 047]  average training loss: 2317.3108
cellbender:remove-background: [epoch 048]  average training loss: 2347.9577
cellbender:remove-background: [epoch 049]  average training loss: 2349.8315
cellbender:remove-background: [epoch 050]  average training loss: 2363.4249
cellbender:remove-background: [epoch 050] average test loss: 2376.7486
cellbender:remove-background: [epoch 051]  average training loss: 2340.2712
cellbender:remove-background: [epoch 052]  average training loss: 2352.8333
cellbender:remove-background: [epoch 053]  average training loss: 2379.7733
cellbender:remove-background: [epoch 054]  average training loss: 2365.1577
cellbender:remove-background: [epoch 055]  average training loss: 2409.8681
cellbender:remove-background: [epoch 055] average test loss: 2395.8247
cellbender:remove-background: [epoch 056]  average training loss: 2395.5296
cellbender:remove-background: [epoch 057]  average training loss: 2410.3034
cellbender:remove-background: [epoch 058]  average training loss: 2408.6935
cellbender:remove-background: [epoch 059]  average training loss: 2392.3087
cellbender:remove-background: [epoch 060]  average training loss: 2376.6829
cellbender:remove-background: [epoch 060] average test loss: 2409.3561
cellbender:remove-background: [epoch 061]  average training loss: 2372.3016
cellbender:remove-background: [epoch 062]  average training loss: 2420.0193
cellbender:remove-background: [epoch 063]  average training loss: 2374.2914
cellbender:remove-background: [epoch 064]  average training loss: 2404.2584
cellbender:remove-background: [epoch 065]  average training loss: 2378.0126
cellbender:remove-background: [epoch 065] average test loss: 2365.1094
cellbender:remove-background: [epoch 066]  average training loss: 2382.2166
cellbender:remove-background: [epoch 067]  average training loss: 2357.6782
cellbender:remove-background: [epoch 068]  average training loss: 2373.2432
cellbender:remove-background: [epoch 069]  average training loss: 2401.2723
cellbender:remove-background: [epoch 070]  average training loss: 2355.0374
cellbender:remove-background: [epoch 070] average test loss: 2381.1293
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/2673-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 071]  average training loss: 2364.5291
cellbender:remove-background: [epoch 072]  average training loss: 2363.9378
cellbender:remove-background: [epoch 073]  average training loss: 2378.3177
cellbender:remove-background: [epoch 074]  average training loss: 2372.5276
cellbender:remove-background: [epoch 075]  average training loss: 2402.0836
cellbender:remove-background: [epoch 075] average test loss: 2432.2977
cellbender:remove-background: [epoch 076]  average training loss: 2375.5795
cellbender:remove-background: [epoch 077]  average training loss: 2373.2533
cellbender:remove-background: [epoch 078]  average training loss: 2377.5160
cellbender:remove-background: [epoch 079]  average training loss: 2372.4059
cellbender:remove-background: [epoch 080]  average training loss: 2383.1812
cellbender:remove-background: [epoch 080] average test loss: 2425.0100
cellbender:remove-background: [epoch 081]  average training loss: 2377.4644
cellbender:remove-background: [epoch 082]  average training loss: 2380.4637
cellbender:remove-background: [epoch 083]  average training loss: 2371.1557
cellbender:remove-background: [epoch 084]  average training loss: 2378.2379
cellbender:remove-background: [epoch 085]  average training loss: 2372.0791
cellbender:remove-background: [epoch 085] average test loss: 2408.2077
cellbender:remove-background: [epoch 086]  average training loss: 2375.7633
cellbender:remove-background: [epoch 087]  average training loss: 2374.3617
cellbender:remove-background: [epoch 088]  average training loss: 2375.3152
cellbender:remove-background: [epoch 089]  average training loss: 2370.8599
cellbender:remove-background: [epoch 090]  average training loss: 2396.3400
cellbender:remove-background: [epoch 090] average test loss: 2426.9840
cellbender:remove-background: [epoch 091]  average training loss: 2383.1991
cellbender:remove-background: [epoch 092]  average training loss: 2404.2808
cellbender:remove-background: [epoch 093]  average training loss: 2365.2342
cellbender:remove-background: [epoch 094]  average training loss: 2386.4205
cellbender:remove-background: [epoch 095]  average training loss: 2382.7081
cellbender:remove-background: [epoch 095] average test loss: 2531.5439
cellbender:remove-background: [epoch 096]  average training loss: 2385.9704
cellbender:remove-background: [epoch 097]  average training loss: 2393.7875
cellbender:remove-background: [epoch 098]  average training loss: 2377.0082
cellbender:remove-background: [epoch 099]  average training loss: 2373.7082
cellbender:remove-background: [epoch 100]  average training loss: 2356.8364
cellbender:remove-background: [epoch 100] average test loss: 2455.6977
cellbender:remove-background: [epoch 101]  average training loss: 2398.8594
cellbender:remove-background: [epoch 102]  average training loss: 2374.9430
cellbender:remove-background: [epoch 103]  average training loss: 2373.3556
cellbender:remove-background: [epoch 104]  average training loss: 2383.8235
cellbender:remove-background: [epoch 105]  average training loss: 2388.8603
cellbender:remove-background: [epoch 105] average test loss: 2402.3857
cellbender:remove-background: [epoch 106]  average training loss: 2398.6658
cellbender:remove-background: [epoch 107]  average training loss: 2372.3622
cellbender:remove-background: [epoch 108]  average training loss: 2384.2800
cellbender:remove-background: [epoch 109]  average training loss: 2378.5633
cellbender:remove-background: [epoch 110]  average training loss: 2382.6583
cellbender:remove-background: [epoch 110] average test loss: 2423.0731
cellbender:remove-background: [epoch 111]  average training loss: 2401.6037
cellbender:remove-background: [epoch 112]  average training loss: 2398.0755
cellbender:remove-background: [epoch 113]  average training loss: 2372.7579
cellbender:remove-background: [epoch 114]  average training loss: 2367.6336
cellbender:remove-background: [epoch 115]  average training loss: 2391.3819
cellbender:remove-background: [epoch 115] average test loss: 2449.3195
cellbender:remove-background: [epoch 116]  average training loss: 2354.8109
cellbender:remove-background: [epoch 117]  average training loss: 2368.8466
cellbender:remove-background: [epoch 118]  average training loss: 2373.9453
cellbender:remove-background: [epoch 119]  average training loss: 2355.5366
cellbender:remove-background: [epoch 120]  average training loss: 2378.4212
cellbender:remove-background: [epoch 120] average test loss: 2503.0641
cellbender:remove-background: [epoch 121]  average training loss: 2386.1036
cellbender:remove-background: [epoch 122]  average training loss: 2377.2272
cellbender:remove-background: [epoch 123]  average training loss: 2379.6310
cellbender:remove-background: [epoch 124]  average training loss: 2360.9553
cellbender:remove-background: [epoch 125]  average training loss: 2381.8054
cellbender:remove-background: [epoch 125] average test loss: 2434.4999
cellbender:remove-background: [epoch 126]  average training loss: 2365.2880
cellbender:remove-background: [epoch 127]  average training loss: 2375.7898
cellbender:remove-background: [epoch 128]  average training loss: 2364.6541
cellbender:remove-background: [epoch 129]  average training loss: 2383.3917
cellbender:remove-background: [epoch 130]  average training loss: 2388.2388
cellbender:remove-background: [epoch 130] average test loss: 2567.7224
cellbender:remove-background: [epoch 131]  average training loss: 2365.1710
cellbender:remove-background: [epoch 132]  average training loss: 2385.7062
cellbender:remove-background: [epoch 133]  average training loss: 2385.4531
cellbender:remove-background: [epoch 134]  average training loss: 2380.6469
cellbender:remove-background: [epoch 135]  average training loss: 2377.9564
cellbender:remove-background: [epoch 135] average test loss: 2452.0788
cellbender:remove-background: [epoch 136]  average training loss: 2360.8632
cellbender:remove-background: [epoch 137]  average training loss: 2370.7653
cellbender:remove-background: [epoch 138]  average training loss: 2387.9379
cellbender:remove-background: [epoch 139]  average training loss: 2349.7484
cellbender:remove-background: [epoch 140]  average training loss: 2366.2510
cellbender:remove-background: [epoch 140] average test loss: 2474.3495
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/2673-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 141]  average training loss: 2362.7272
cellbender:remove-background: [epoch 142]  average training loss: 2358.5121
cellbender:remove-background: [epoch 143]  average training loss: 2365.5608
cellbender:remove-background: [epoch 144]  average training loss: 2366.2895
cellbender:remove-background: [epoch 145]  average training loss: 2360.7941
cellbender:remove-background: [epoch 145] average test loss: 2440.5671
cellbender:remove-background: [epoch 146]  average training loss: 2365.5766
cellbender:remove-background: [epoch 147]  average training loss: 2375.3143
cellbender:remove-background: [epoch 148]  average training loss: 2364.4161
cellbender:remove-background: [epoch 149]  average training loss: 2375.8201
cellbender:remove-background: [epoch 150]  average training loss: 2375.6762
cellbender:remove-background: [epoch 150] average test loss: 2492.4669
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/2673-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:30:35
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp1hnyk_61
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp1hnyk_61
/tmp/tmp1hnyk_61/eb932317f5_random.pyro
/tmp/tmp1hnyk_61/eb932317f5_random.cuda
/tmp/tmp1hnyk_61/eb932317f5_model.torch
/tmp/tmp1hnyk_61/eb932317f5_optim.torch
/tmp/tmp1hnyk_61/eb932317f5_optim.pyro
/tmp/tmp1hnyk_61/eb932317f5_params.pyro
/tmp/tmp1hnyk_61/eb932317f5_train.loaderstate
/tmp/tmp1hnyk_61/eb932317f5_test.loaderstate
/tmp/tmp1hnyk_61/eb932317f5_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 (1/47)
cellbender:remove-background:     [0.03 mins per chunk]
cellbender:remove-background: Working on chunk (2/47)
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cellbender:remove-background: Working on chunk (44/47)
cellbender:remove-background: Working on chunk (45/47)
cellbender:remove-background: Working on chunk (46/47)
cellbender:remove-background: Working on chunk (47/47)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2673-Bipolar-DLPFC/2673-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/2673-Bipolar-DLPFC/2673-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:34:09

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2673-Bipolar-DLPFC/2673-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/2673-Bipolar-DLPFC/2673-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:     [1.47 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 15:44:52 Total MCKP estimation time = 619.02 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/2673-Bipolar-DLPFC/2673-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/2673-Bipolar-DLPFC/2673-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/2673-Bipolar-DLPFC/2673-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/2673-Bipolar-DLPFC/2673-Bipolar-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:45:09