cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1227-Control-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-dACC/1227-Control-dACC.cellbender.output.h5 --cuda --expected-cells 11040 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 37e927f860)
cellbender:remove-background: 2024-06-06 15:04:06
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/1227-Control-dACC.raw_feature_bc_matrix.h5
cellbender:remove-background: CellRanger v3 format
cellbender:remove-background: Features in dataset: 36601 Gene Expression
cellbender:remove-background: Trimming features for inference.
cellbender:remove-background: 32941 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 4669
cellbender:remove-background: Prior on counts for empty droplets is 248
cellbender:remove-background: Excluding 5351 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 27590 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 124
cellbender:remove-background: Using 11040 probable cell barcodes, plus an additional 8960 barcodes, and 31788 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 244 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp_94_ltjq
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: 9912.8568
cellbender:remove-background: [epoch 002]  average training loss: 7679.4076  (6.1 seconds per epoch)
cellbender:remove-background: Will checkpoint every 70 epochs
cellbender:remove-background: [epoch 003]  average training loss: 6480.7457
cellbender:remove-background: [epoch 004]  average training loss: 5709.8504
cellbender:remove-background: [epoch 005]  average training loss: 5507.2074
cellbender:remove-background: [epoch 005] average test loss: 5723.5267
cellbender:remove-background: [epoch 006]  average training loss: 5419.8547
cellbender:remove-background: [epoch 007]  average training loss: 5356.0012
cellbender:remove-background: [epoch 008]  average training loss: 5276.3943
cellbender:remove-background: [epoch 009]  average training loss: 5264.5429
cellbender:remove-background: [epoch 010]  average training loss: 5193.0452
cellbender:remove-background: [epoch 010] average test loss: 5224.8152
cellbender:remove-background: [epoch 011]  average training loss: 5191.9037
cellbender:remove-background: [epoch 012]  average training loss: 4976.5293
cellbender:remove-background: [epoch 013]  average training loss: 4776.1469
cellbender:remove-background: [epoch 014]  average training loss: 4778.2805
cellbender:remove-background: [epoch 015]  average training loss: 4708.5058
cellbender:remove-background: [epoch 015] average test loss: 4758.1914
cellbender:remove-background: [epoch 016]  average training loss: 4673.4449
cellbender:remove-background: [epoch 017]  average training loss: 4677.7578
cellbender:remove-background: [epoch 018]  average training loss: 4644.6489
cellbender:remove-background: [epoch 019]  average training loss: 4608.8810
cellbender:remove-background: [epoch 020]  average training loss: 4556.8204
cellbender:remove-background: [epoch 020] average test loss: 4605.5134
cellbender:remove-background: [epoch 021]  average training loss: 4540.0527
cellbender:remove-background: [epoch 022]  average training loss: 4524.7794
cellbender:remove-background: [epoch 023]  average training loss: 4511.9385
cellbender:remove-background: [epoch 024]  average training loss: 4490.2280
cellbender:remove-background: [epoch 025]  average training loss: 4482.9751
cellbender:remove-background: [epoch 025] average test loss: 4494.2555
cellbender:remove-background: [epoch 026]  average training loss: 4451.8591
cellbender:remove-background: [epoch 027]  average training loss: 4449.2150
cellbender:remove-background: [epoch 028]  average training loss: 4447.0683
cellbender:remove-background: [epoch 029]  average training loss: 4431.3114
cellbender:remove-background: [epoch 030]  average training loss: 4424.9069
cellbender:remove-background: [epoch 030] average test loss: 4404.1333
cellbender:remove-background: [epoch 031]  average training loss: 4425.8818
cellbender:remove-background: [epoch 032]  average training loss: 4424.9231
cellbender:remove-background: [epoch 033]  average training loss: 4414.2601
cellbender:remove-background: [epoch 034]  average training loss: 4411.7438
cellbender:remove-background: [epoch 035]  average training loss: 4405.4073
cellbender:remove-background: [epoch 035] average test loss: 4384.5146
cellbender:remove-background: [epoch 036]  average training loss: 4404.2134
cellbender:remove-background: [epoch 037]  average training loss: 4400.9603
cellbender:remove-background: [epoch 038]  average training loss: 4395.2330
cellbender:remove-background: [epoch 039]  average training loss: 4394.1319
cellbender:remove-background: [epoch 040]  average training loss: 4388.9302
cellbender:remove-background: [epoch 040] average test loss: 4388.9494
cellbender:remove-background: [epoch 041]  average training loss: 4390.6819
cellbender:remove-background: [epoch 042]  average training loss: 4387.2903
cellbender:remove-background: [epoch 043]  average training loss: 4385.8670
cellbender:remove-background: [epoch 044]  average training loss: 4382.1177
cellbender:remove-background: [epoch 045]  average training loss: 4380.2224
cellbender:remove-background: [epoch 045] average test loss: 4378.3459
cellbender:remove-background: [epoch 046]  average training loss: 4379.7989
cellbender:remove-background: [epoch 047]  average training loss: 4375.8279
cellbender:remove-background: [epoch 048]  average training loss: 4376.6338
cellbender:remove-background: [epoch 049]  average training loss: 4374.8957
cellbender:remove-background: [epoch 050]  average training loss: 4369.3466
cellbender:remove-background: [epoch 050] average test loss: 4376.8308
cellbender:remove-background: [epoch 051]  average training loss: 4368.1038
cellbender:remove-background: [epoch 052]  average training loss: 4369.4771
cellbender:remove-background: [epoch 053]  average training loss: 4371.8110
cellbender:remove-background: [epoch 054]  average training loss: 4365.9737
cellbender:remove-background: [epoch 055]  average training loss: 4368.4429
cellbender:remove-background: [epoch 055] average test loss: 4380.3363
cellbender:remove-background: [epoch 056]  average training loss: 4365.1590
cellbender:remove-background: [epoch 057]  average training loss: 4364.6973
cellbender:remove-background: [epoch 058]  average training loss: 4366.2616
cellbender:remove-background: [epoch 059]  average training loss: 4361.5068
cellbender:remove-background: [epoch 060]  average training loss: 4362.4482
cellbender:remove-background: [epoch 060] average test loss: 4381.6290
cellbender:remove-background: [epoch 061]  average training loss: 4370.1607
cellbender:remove-background: [epoch 062]  average training loss: 4359.3107
cellbender:remove-background: [epoch 063]  average training loss: 4365.1520
cellbender:remove-background: [epoch 064]  average training loss: 4362.5882
cellbender:remove-background: [epoch 065]  average training loss: 4370.1495
cellbender:remove-background: [epoch 065] average test loss: 4378.7689
cellbender:remove-background: [epoch 066]  average training loss: 4376.4202
cellbender:remove-background: [epoch 067]  average training loss: 4380.7662
cellbender:remove-background: [epoch 068]  average training loss: 4372.2748
cellbender:remove-background: [epoch 069]  average training loss: 4390.0895
cellbender:remove-background: [epoch 070]  average training loss: 4399.6933
cellbender:remove-background: [epoch 070] average test loss: 4406.0442
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/1227-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 071]  average training loss: 4407.0824
cellbender:remove-background: [epoch 072]  average training loss: 4406.9155
cellbender:remove-background: [epoch 073]  average training loss: 4420.5766
cellbender:remove-background: [epoch 074]  average training loss: 4437.4820
cellbender:remove-background: [epoch 075]  average training loss: 4457.5688
cellbender:remove-background: [epoch 075] average test loss: 4489.9426
cellbender:remove-background: [epoch 076]  average training loss: 4470.2959
cellbender:remove-background: [epoch 077]  average training loss: 4486.7541
cellbender:remove-background: [epoch 078]  average training loss: 4471.4729
cellbender:remove-background: [epoch 079]  average training loss: 4492.9048
cellbender:remove-background: [epoch 080]  average training loss: 4506.0498
cellbender:remove-background: [epoch 080] average test loss: 4613.6173
cellbender:remove-background: [epoch 081]  average training loss: 4493.8604
cellbender:remove-background: [epoch 082]  average training loss: 4518.4044
cellbender:remove-background: [epoch 083]  average training loss: 4480.5231
cellbender:remove-background: [epoch 084]  average training loss: 4494.2599
cellbender:remove-background: [epoch 085]  average training loss: 4437.3001
cellbender:remove-background: [epoch 085] average test loss: 4543.2862
cellbender:remove-background: [epoch 086]  average training loss: 4462.3406
cellbender:remove-background: [epoch 087]  average training loss: 4459.4692
cellbender:remove-background: [epoch 088]  average training loss: 4464.1495
cellbender:remove-background: [epoch 089]  average training loss: 4488.0858
cellbender:remove-background: [epoch 090]  average training loss: 4453.8651
cellbender:remove-background: [epoch 090] average test loss: 4457.3090
cellbender:remove-background: [epoch 091]  average training loss: 4446.6303
cellbender:remove-background: [epoch 092]  average training loss: 4513.4459
cellbender:remove-background: [epoch 093]  average training loss: 4462.7604
cellbender:remove-background: [epoch 094]  average training loss: 4474.6089
cellbender:remove-background: [epoch 095]  average training loss: 4490.1379
cellbender:remove-background: [epoch 095] average test loss: 4523.1369
cellbender:remove-background: [epoch 096]  average training loss: 4492.8649
cellbender:remove-background: [epoch 097]  average training loss: 4499.5008
cellbender:remove-background: [epoch 098]  average training loss: 4482.2152
cellbender:remove-background: [epoch 099]  average training loss: 4467.7722
cellbender:remove-background: [epoch 100]  average training loss: 4491.3776
cellbender:remove-background: [epoch 100] average test loss: 4481.8843
cellbender:remove-background: [epoch 101]  average training loss: 4453.2556
cellbender:remove-background: [epoch 102]  average training loss: 4467.2133
cellbender:remove-background: [epoch 103]  average training loss: 4472.0506
cellbender:remove-background: [epoch 104]  average training loss: 4447.7842
cellbender:remove-background: [epoch 105]  average training loss: 4449.3964
cellbender:remove-background: [epoch 105] average test loss: 4514.7451
cellbender:remove-background: [epoch 106]  average training loss: 4449.9256
cellbender:remove-background: [epoch 107]  average training loss: 4444.7224
cellbender:remove-background: [epoch 108]  average training loss: 4472.0203
cellbender:remove-background: [epoch 109]  average training loss: 4464.8878
cellbender:remove-background: [epoch 110]  average training loss: 4477.0056
cellbender:remove-background: [epoch 110] average test loss: 4481.3802
cellbender:remove-background: [epoch 111]  average training loss: 4463.1967
cellbender:remove-background: [epoch 112]  average training loss: 4482.2446
cellbender:remove-background: [epoch 113]  average training loss: 4459.4072
cellbender:remove-background: [epoch 114]  average training loss: 4463.5555
cellbender:remove-background: [epoch 115]  average training loss: 4458.2840
cellbender:remove-background: [epoch 115] average test loss: 4481.2487
cellbender:remove-background: [epoch 116]  average training loss: 4462.1133
cellbender:remove-background: [epoch 117]  average training loss: 4457.6199
cellbender:remove-background: [epoch 118]  average training loss: 4458.4021
cellbender:remove-background: [epoch 119]  average training loss: 4466.2814
cellbender:remove-background: [epoch 120]  average training loss: 4473.8289
cellbender:remove-background: [epoch 120] average test loss: 4557.3204
cellbender:remove-background: [epoch 121]  average training loss: 4445.9340
cellbender:remove-background: [epoch 122]  average training loss: 4461.2365
cellbender:remove-background: [epoch 123]  average training loss: 4474.5786
cellbender:remove-background: [epoch 124]  average training loss: 4451.9232
cellbender:remove-background: [epoch 125]  average training loss: 4439.3344
cellbender:remove-background: [epoch 125] average test loss: 4554.7022
cellbender:remove-background: [epoch 126]  average training loss: 4444.1708
cellbender:remove-background: [epoch 127]  average training loss: 4463.6107
cellbender:remove-background: [epoch 128]  average training loss: 4457.8583
cellbender:remove-background: [epoch 129]  average training loss: 4459.0644
cellbender:remove-background: [epoch 130]  average training loss: 4450.3715
cellbender:remove-background: [epoch 130] average test loss: 4553.1416
cellbender:remove-background: [epoch 131]  average training loss: 4441.8129
cellbender:remove-background: [epoch 132]  average training loss: 4445.0410
cellbender:remove-background: [epoch 133]  average training loss: 4444.8663
cellbender:remove-background: [epoch 134]  average training loss: 4445.4185
cellbender:remove-background: [epoch 135]  average training loss: 4468.6697
cellbender:remove-background: [epoch 135] average test loss: 4531.4234
cellbender:remove-background: [epoch 136]  average training loss: 4448.4130
cellbender:remove-background: [epoch 137]  average training loss: 4436.4307
cellbender:remove-background: [epoch 138]  average training loss: 4428.4484
cellbender:remove-background: [epoch 139]  average training loss: 4449.0383
cellbender:remove-background: [epoch 140]  average training loss: 4443.3532
cellbender:remove-background: [epoch 140] average test loss: 4486.5074
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/1227-Control-dACC/ckpt.tar.gz
cellbender:remove-background: [epoch 141]  average training loss: 4444.9815
cellbender:remove-background: [epoch 142]  average training loss: 4426.2856
cellbender:remove-background: [epoch 143]  average training loss: 4481.5029
cellbender:remove-background: [epoch 144]  average training loss: 4439.3028
cellbender:remove-background: [epoch 145]  average training loss: 4463.6575
cellbender:remove-background: [epoch 145] average test loss: 4554.1998
cellbender:remove-background: [epoch 146]  average training loss: 4447.5286
cellbender:remove-background: [epoch 147]  average training loss: 4433.6560
cellbender:remove-background: [epoch 148]  average training loss: 4471.5318
cellbender:remove-background: [epoch 149]  average training loss: 4441.8541
cellbender:remove-background: [epoch 150]  average training loss: 4436.7510
cellbender:remove-background: [epoch 150] average test loss: 4486.6126
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/1227-Control-dACC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:24:00
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp_4rv3_kw
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp_4rv3_kw
/tmp/tmp_4rv3_kw/37e927f860_random.pyro
/tmp/tmp_4rv3_kw/37e927f860_random.cuda
/tmp/tmp_4rv3_kw/37e927f860_model.torch
/tmp/tmp_4rv3_kw/37e927f860_optim.torch
/tmp/tmp_4rv3_kw/37e927f860_optim.pyro
/tmp/tmp_4rv3_kw/37e927f860_params.pyro
/tmp/tmp_4rv3_kw/37e927f860_train.loaderstate
/tmp/tmp_4rv3_kw/37e927f860_test.loaderstate
/tmp/tmp_4rv3_kw/37e927f860_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 (1/115)
cellbender:remove-background:     [0.06 mins per chunk]
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cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-dACC/1227-Control-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-dACC/1227-Control-dACC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:32:57

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-dACC/1227-Control-dACC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-dACC/1227-Control-dACC.cellbender.output_cell_barcodes.csv
cellbender:remove-background: Computing target noise counts per gene for MCKP estimator
cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01
cellbender:remove-background: Computing denoised counts using mckp estimator
cellbender:remove-background: Working on chunk (1/7)
cellbender:remove-background:     [2.28 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 15:49:50 Total MCKP estimation time = 965.46 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/1227-Control-dACC/1227-Control-dACC.cellbender.output.h5
cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-dACC/1227-Control-dACC.cellbender.output_filtered.h5
cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-dACC/1227-Control-dACC.cellbender.output_metrics.csv
Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    from lxml.html.clean import clean_html
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in <module>
    ) from None
ImportError: lxml.html.clean module is now a separate project lxml_html_clean.
Install lxml[html_clean] or lxml_html_clean directly.
Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    from lxml.html.clean import clean_html
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/lxml/html/clean.py", line 21, in <module>
    ) from None
ImportError: lxml.html.clean module is now a separate project lxml_html_clean.
Install lxml[html_clean] or lxml_html_clean directly.
mv: cannot stat ‘tmp.report.nbconvert.html’: No such file or directory
rm: cannot remove ‘tmp.report.nbconvert.ipynb’: No such file or directory
cellbender:remove-background: Unable to create report.
cellbender:remove-background: Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/run.py", line 351, in compute_output_denoised_counts_reports_metrics
    output=html_report_file,
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 82, in run_notebook_make_html
    title=('CellBender: ' + os.path.basename(output).replace('_report.html', '')),
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/remove_background/report.py", line 59, in _postprocess_html
    with open(file, mode='r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1227-Control-dACC/1227-Control-dACC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:50:13