cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1303-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1303-Schizophrenia-Hippocampus/1303-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 20000 --total-droplets-included 21000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 257a69300d)
cellbender:remove-background: 2024-06-06 15:12:35
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/1303-Schizophrenia-Hippocampus.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: 30516 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 862
cellbender:remove-background: Prior on counts for empty droplets is 383
cellbender:remove-background: Excluding 2505 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 28011 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 191
cellbender:remove-background: Using 20000 probable cell barcodes, plus an additional 1000 barcodes, and 15104 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 378 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpt9jtfuxj
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: 3064.6947
cellbender:remove-background: [epoch 002]  average training loss: 2853.8312  (8.1 seconds per epoch)
cellbender:remove-background: Will checkpoint every 52 epochs
cellbender:remove-background: [epoch 003]  average training loss: 2709.6436
cellbender:remove-background: [epoch 004]  average training loss: 2585.9358
cellbender:remove-background: [epoch 005]  average training loss: 2507.1192
cellbender:remove-background: [epoch 005] average test loss: 2474.6514
cellbender:remove-background: [epoch 006]  average training loss: 2469.9109
cellbender:remove-background: [epoch 007]  average training loss: 2459.9495
cellbender:remove-background: [epoch 008]  average training loss: 2441.9749
cellbender:remove-background: [epoch 009]  average training loss: 2436.3765
cellbender:remove-background: [epoch 010]  average training loss: 2433.1676
cellbender:remove-background: [epoch 010] average test loss: 2429.3129
cellbender:remove-background: [epoch 011]  average training loss: 2427.2684
cellbender:remove-background: [epoch 012]  average training loss: 2423.1600
cellbender:remove-background: [epoch 013]  average training loss: 2429.1493
cellbender:remove-background: [epoch 014]  average training loss: 2423.7224
cellbender:remove-background: [epoch 015]  average training loss: 2423.8437
cellbender:remove-background: [epoch 015] average test loss: 2422.0288
cellbender:remove-background: [epoch 016]  average training loss: 2424.7656
cellbender:remove-background: [epoch 017]  average training loss: 2424.3767
cellbender:remove-background: [epoch 018]  average training loss: 2419.5129
cellbender:remove-background: [epoch 019]  average training loss: 2420.8190
cellbender:remove-background: [epoch 020]  average training loss: 2421.0077
cellbender:remove-background: [epoch 020] average test loss: 2413.3970
cellbender:remove-background: [epoch 021]  average training loss: 2422.2393
cellbender:remove-background: [epoch 022]  average training loss: 2421.3994
cellbender:remove-background: [epoch 023]  average training loss: 2420.5784
cellbender:remove-background: [epoch 024]  average training loss: 2421.1709
cellbender:remove-background: [epoch 025]  average training loss: 2421.5947
cellbender:remove-background: [epoch 025] average test loss: 2411.4448
cellbender:remove-background: [epoch 026]  average training loss: 2419.8805
cellbender:remove-background: [epoch 027]  average training loss: 2421.0447
cellbender:remove-background: [epoch 028]  average training loss: 2420.2538
cellbender:remove-background: [epoch 029]  average training loss: 2419.3438
cellbender:remove-background: [epoch 030]  average training loss: 2420.7692
cellbender:remove-background: [epoch 030] average test loss: 2414.0980
cellbender:remove-background: [epoch 031]  average training loss: 2419.1830
cellbender:remove-background: [epoch 032]  average training loss: 2420.4656
cellbender:remove-background: [epoch 033]  average training loss: 2420.3578
cellbender:remove-background: [epoch 034]  average training loss: 2418.7503
cellbender:remove-background: [epoch 035]  average training loss: 2421.7351
cellbender:remove-background: [epoch 035] average test loss: 2415.5278
cellbender:remove-background: [epoch 036]  average training loss: 2420.8468
cellbender:remove-background: [epoch 037]  average training loss: 2421.9582
cellbender:remove-background: [epoch 038]  average training loss: 2421.0523
cellbender:remove-background: [epoch 039]  average training loss: 2420.8429
cellbender:remove-background: [epoch 040]  average training loss: 2419.2617
cellbender:remove-background: [epoch 040] average test loss: 2410.9450
cellbender:remove-background: [epoch 041]  average training loss: 2416.2439
cellbender:remove-background: [epoch 042]  average training loss: 2417.7968
cellbender:remove-background: [epoch 043]  average training loss: 2418.8171
cellbender:remove-background: [epoch 044]  average training loss: 2419.8395
cellbender:remove-background: [epoch 045]  average training loss: 2425.0048
cellbender:remove-background: [epoch 045] average test loss: 2414.3021
cellbender:remove-background: [epoch 046]  average training loss: 2423.3281
cellbender:remove-background: [epoch 047]  average training loss: 2423.6438
cellbender:remove-background: [epoch 048]  average training loss: 2424.3564
cellbender:remove-background: [epoch 049]  average training loss: 2428.4909
cellbender:remove-background: [epoch 050]  average training loss: 2423.9967
cellbender:remove-background: [epoch 050] average test loss: 2401.1878
cellbender:remove-background: [epoch 051]  average training loss: 2428.4620
cellbender:remove-background: [epoch 052]  average training loss: 2422.2956
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/1303-Schizophrenia-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 053]  average training loss: 2428.8962
cellbender:remove-background: [epoch 054]  average training loss: 2426.2024
cellbender:remove-background: [epoch 055]  average training loss: 2426.7469
cellbender:remove-background: [epoch 055] average test loss: 2413.9228
cellbender:remove-background: [epoch 056]  average training loss: 2432.9665
cellbender:remove-background: [epoch 057]  average training loss: 2424.5179
cellbender:remove-background: [epoch 058]  average training loss: 2426.5071
cellbender:remove-background: [epoch 059]  average training loss: 2429.2079
cellbender:remove-background: [epoch 060]  average training loss: 2429.1315
cellbender:remove-background: [epoch 060] average test loss: 2413.1238
cellbender:remove-background: [epoch 061]  average training loss: 2432.5594
cellbender:remove-background: [epoch 062]  average training loss: 2429.1437
cellbender:remove-background: [epoch 063]  average training loss: 2429.7382
cellbender:remove-background: [epoch 064]  average training loss: 2435.9852
cellbender:remove-background: [epoch 065]  average training loss: 2432.3508
cellbender:remove-background: [epoch 065] average test loss: 2433.2380
cellbender:remove-background: [epoch 066]  average training loss: 2433.9671
cellbender:remove-background: [epoch 067]  average training loss: 2438.0810
cellbender:remove-background: [epoch 068]  average training loss: 2437.6569
cellbender:remove-background: [epoch 069]  average training loss: 2433.5897
cellbender:remove-background: [epoch 070]  average training loss: 2434.1634
cellbender:remove-background: [epoch 070] average test loss: 2417.4582
cellbender:remove-background: [epoch 071]  average training loss: 2442.0547
cellbender:remove-background: [epoch 072]  average training loss: 2433.4150
cellbender:remove-background: [epoch 073]  average training loss: 2439.8443
cellbender:remove-background: [epoch 074]  average training loss: 2432.5009
cellbender:remove-background: [epoch 075]  average training loss: 2433.4585
cellbender:remove-background: [epoch 075] average test loss: 2433.9134
cellbender:remove-background: [epoch 076]  average training loss: 2442.0696
cellbender:remove-background: [epoch 077]  average training loss: 2434.9119
cellbender:remove-background: [epoch 078]  average training loss: 2432.5200
cellbender:remove-background: [epoch 079]  average training loss: 2436.2655
cellbender:remove-background: [epoch 080]  average training loss: 2432.6377
cellbender:remove-background: [epoch 080] average test loss: 2417.4327
cellbender:remove-background: [epoch 081]  average training loss: 2431.0799
cellbender:remove-background: [epoch 082]  average training loss: 2435.2788
cellbender:remove-background: [epoch 083]  average training loss: 2432.3608
cellbender:remove-background: [epoch 084]  average training loss: 2436.8367
cellbender:remove-background: [epoch 085]  average training loss: 2435.8914
cellbender:remove-background: [epoch 085] average test loss: 2432.4012
cellbender:remove-background: [epoch 086]  average training loss: 2439.5165
cellbender:remove-background: [epoch 087]  average training loss: 2430.5133
cellbender:remove-background: [epoch 088]  average training loss: 2434.5528
cellbender:remove-background: [epoch 089]  average training loss: 2442.7203
cellbender:remove-background: [epoch 090]  average training loss: 2441.7014
cellbender:remove-background: [epoch 090] average test loss: 2437.6475
cellbender:remove-background: [epoch 091]  average training loss: 2441.7909
cellbender:remove-background: [epoch 092]  average training loss: 2439.8890
cellbender:remove-background: [epoch 093]  average training loss: 2437.3724
cellbender:remove-background: [epoch 094]  average training loss: 2436.8055
cellbender:remove-background: [epoch 095]  average training loss: 2435.7497
cellbender:remove-background: [epoch 095] average test loss: 2427.8061
cellbender:remove-background: [epoch 096]  average training loss: 2443.1590
cellbender:remove-background: [epoch 097]  average training loss: 2441.9719
cellbender:remove-background: [epoch 098]  average training loss: 2443.2203
cellbender:remove-background: [epoch 099]  average training loss: 2437.3270
cellbender:remove-background: [epoch 100]  average training loss: 2443.9610
cellbender:remove-background: [epoch 100] average test loss: 2436.3675
cellbender:remove-background: [epoch 101]  average training loss: 2439.9675
cellbender:remove-background: [epoch 102]  average training loss: 2442.6051
cellbender:remove-background: [epoch 103]  average training loss: 2438.0604
cellbender:remove-background: [epoch 104]  average training loss: 2431.0358
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/1303-Schizophrenia-Hippocampus/ckpt.tar.gz
cellbender:remove-background: [epoch 105]  average training loss: 2439.6158
cellbender:remove-background: [epoch 105] average test loss: 2449.8511
cellbender:remove-background: [epoch 106]  average training loss: 2441.4640
cellbender:remove-background: [epoch 107]  average training loss: 2443.0936
cellbender:remove-background: [epoch 108]  average training loss: 2439.2521
cellbender:remove-background: [epoch 109]  average training loss: 2439.9485
cellbender:remove-background: [epoch 110]  average training loss: 2440.2157
cellbender:remove-background: [epoch 110] average test loss: 2435.4567
cellbender:remove-background: [epoch 111]  average training loss: 2440.3978
cellbender:remove-background: [epoch 112]  average training loss: 2438.1909
cellbender:remove-background: [epoch 113]  average training loss: 2440.7000
cellbender:remove-background: [epoch 114]  average training loss: 2438.2499
cellbender:remove-background: [epoch 115]  average training loss: 2435.9836
cellbender:remove-background: [epoch 115] average test loss: 2438.0150
cellbender:remove-background: [epoch 116]  average training loss: 2438.5165
cellbender:remove-background: [epoch 117]  average training loss: 2442.9324
cellbender:remove-background: [epoch 118]  average training loss: 2437.3241
cellbender:remove-background: [epoch 119]  average training loss: 2440.9187
cellbender:remove-background: [epoch 120]  average training loss: 2440.2900
cellbender:remove-background: [epoch 120] average test loss: 2439.2847
cellbender:remove-background: [epoch 121]  average training loss: 2437.8755
cellbender:remove-background: [epoch 122]  average training loss: 2437.3735
cellbender:remove-background: [epoch 123]  average training loss: 2441.4592
cellbender:remove-background: [epoch 124]  average training loss: 2441.9693
cellbender:remove-background: [epoch 125]  average training loss: 2440.1170
cellbender:remove-background: [epoch 125] average test loss: 2438.2938
cellbender:remove-background: [epoch 126]  average training loss: 2439.9943
cellbender:remove-background: [epoch 127]  average training loss: 2437.7368
cellbender:remove-background: [epoch 128]  average training loss: 2442.4912
cellbender:remove-background: [epoch 129]  average training loss: 2442.0093
cellbender:remove-background: [epoch 130]  average training loss: 2442.7050
cellbender:remove-background: [epoch 130] average test loss: 2440.2078
cellbender:remove-background: [epoch 131]  average training loss: 2441.5490
cellbender:remove-background: [epoch 132]  average training loss: 2439.4439
cellbender:remove-background: [epoch 133]  average training loss: 2437.3127
cellbender:remove-background: [epoch 134]  average training loss: 2440.1884
cellbender:remove-background: [epoch 135]  average training loss: 2439.4504
cellbender:remove-background: [epoch 135] average test loss: 2442.5275
cellbender:remove-background: [epoch 136]  average training loss: 2438.2455
cellbender:remove-background: [epoch 137]  average training loss: 2440.7766
cellbender:remove-background: [epoch 138]  average training loss: 2438.4271
cellbender:remove-background: [epoch 139]  average training loss: 2438.5103
cellbender:remove-background: [epoch 140]  average training loss: 2442.0026
cellbender:remove-background: [epoch 140] average test loss: 2437.3128
cellbender:remove-background: [epoch 141]  average training loss: 2438.2399
cellbender:remove-background: [epoch 142]  average training loss: 2437.9155
cellbender:remove-background: [epoch 143]  average training loss: 2437.7675
cellbender:remove-background: [epoch 144]  average training loss: 2437.7924
cellbender:remove-background: [epoch 145]  average training loss: 2438.3143
cellbender:remove-background: [epoch 145] average test loss: 2432.5739
cellbender:remove-background: [epoch 146]  average training loss: 2439.5128
cellbender:remove-background: [epoch 147]  average training loss: 2439.3152
cellbender:remove-background: [epoch 148]  average training loss: 2439.3522
cellbender:remove-background: [epoch 149]  average training loss: 2438.8928
cellbender:remove-background: [epoch 150]  average training loss: 2438.8679
cellbender:remove-background: [epoch 150] average test loss: 2438.6782
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/1303-Schizophrenia-Hippocampus/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:37:12
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmply6xr2t9
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmply6xr2t9
/tmp/tmply6xr2t9/257a69300d_random.pyro
/tmp/tmply6xr2t9/257a69300d_random.cuda
/tmp/tmply6xr2t9/257a69300d_model.torch
/tmp/tmply6xr2t9/257a69300d_optim.torch
/tmp/tmply6xr2t9/257a69300d_optim.pyro
/tmp/tmply6xr2t9/257a69300d_params.pyro
/tmp/tmply6xr2t9/257a69300d_train.loaderstate
/tmp/tmply6xr2t9/257a69300d_test.loaderstate
/tmp/tmply6xr2t9/257a69300d_args.npy
cellbender:remove-background: Posterior not currently included in checkpoint.
cellbender:remove-background: Computing posterior noise count probabilities in mini-batches.
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cellbender:remove-background: Working on chunk (126/129)
cellbender:remove-background: Working on chunk (127/129)
cellbender:remove-background: Working on chunk (128/129)
cellbender:remove-background: Working on chunk (129/129)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1303-Schizophrenia-Hippocampus/1303-Schizophrenia-Hippocampus.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/1303-Schizophrenia-Hippocampus/1303-Schizophrenia-Hippocampus.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:44:16

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1303-Schizophrenia-Hippocampus/1303-Schizophrenia-Hippocampus.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1303-Schizophrenia-Hippocampus/1303-Schizophrenia-Hippocampus.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:     [1.49 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 15:55:04 Total MCKP estimation time = 623.58 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/1303-Schizophrenia-Hippocampus/1303-Schizophrenia-Hippocampus.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/1303-Schizophrenia-Hippocampus/1303-Schizophrenia-Hippocampus.cellbender.output_filtered.h5
cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1303-Schizophrenia-Hippocampus/1303-Schizophrenia-Hippocampus.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/1303-Schizophrenia-Hippocampus/1303-Schizophrenia-Hippocampus.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:55:18