cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2765-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-Hippocampus/2765-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 7923 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash d085eba2f8) cellbender:remove-background: 2024-06-06 15:31:21 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/2765-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: 32000 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 5117 cellbender:remove-background: Prior on counts for empty droplets is 157 cellbender:remove-background: Excluding 7661 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 24339 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 78 cellbender:remove-background: Using 7923 probable cell barcodes, plus an additional 12077 barcodes, and 9884 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 153 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp82kay_od 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: 7603.8521 cellbender:remove-background: [epoch 002] average training loss: 5933.1833 (5.3 seconds per epoch) cellbender:remove-background: Will checkpoint every 80 epochs cellbender:remove-background: [epoch 003] average training loss: 5027.2295 cellbender:remove-background: [epoch 004] average training loss: 4492.7298 cellbender:remove-background: [epoch 005] average training loss: 4335.1369 cellbender:remove-background: [epoch 005] average test loss: 4362.1894 cellbender:remove-background: [epoch 006] average training loss: 4294.0285 cellbender:remove-background: [epoch 007] average training loss: 4228.8278 cellbender:remove-background: [epoch 008] average training loss: 4187.5522 cellbender:remove-background: [epoch 009] average training loss: 4179.7134 cellbender:remove-background: [epoch 010] average training loss: 4083.2084 cellbender:remove-background: [epoch 010] average test loss: 4171.5776 cellbender:remove-background: [epoch 011] average training loss: 3986.1520 cellbender:remove-background: [epoch 012] average training loss: 3938.7880 cellbender:remove-background: [epoch 013] average training loss: 3907.8523 cellbender:remove-background: [epoch 014] average training loss: 3922.7971 cellbender:remove-background: [epoch 015] average training loss: 3883.7452 cellbender:remove-background: [epoch 015] average test loss: 3942.7788 cellbender:remove-background: [epoch 016] average training loss: 3863.2165 cellbender:remove-background: [epoch 017] average training loss: 3878.2096 cellbender:remove-background: [epoch 018] average training loss: 3855.6726 cellbender:remove-background: [epoch 019] average training loss: 3832.6985 cellbender:remove-background: [epoch 020] average training loss: 3808.0987 cellbender:remove-background: [epoch 020] average test loss: 3829.7657 cellbender:remove-background: [epoch 021] average training loss: 3790.4315 cellbender:remove-background: [epoch 022] average training loss: 3767.9610 cellbender:remove-background: [epoch 023] average training loss: 3753.6981 cellbender:remove-background: [epoch 024] average training loss: 3726.8146 cellbender:remove-background: [epoch 025] average training loss: 3733.2329 cellbender:remove-background: [epoch 025] average test loss: 3724.0501 cellbender:remove-background: [epoch 026] average training loss: 3712.4195 cellbender:remove-background: [epoch 027] average training loss: 3708.8792 cellbender:remove-background: [epoch 028] average training loss: 3704.1254 cellbender:remove-background: [epoch 029] average training loss: 3702.0095 cellbender:remove-background: [epoch 030] average training loss: 3693.7078 cellbender:remove-background: [epoch 030] average test loss: 3724.5724 cellbender:remove-background: [epoch 031] average training loss: 3692.5840 cellbender:remove-background: [epoch 032] average training loss: 3677.5447 cellbender:remove-background: [epoch 033] average training loss: 3680.7836 cellbender:remove-background: [epoch 034] average training loss: 3678.3376 cellbender:remove-background: [epoch 035] average training loss: 3681.0895 cellbender:remove-background: [epoch 035] average test loss: 3641.3659 cellbender:remove-background: [epoch 036] average training loss: 3672.8704 cellbender:remove-background: [epoch 037] average training loss: 3681.0070 cellbender:remove-background: [epoch 038] average training loss: 3676.9544 cellbender:remove-background: [epoch 039] average training loss: 3697.6739 cellbender:remove-background: [epoch 040] average training loss: 3688.2718 cellbender:remove-background: [epoch 040] average test loss: 3692.0338 cellbender:remove-background: [epoch 041] average training loss: 3684.6534 cellbender:remove-background: [epoch 042] average training loss: 3713.2001 cellbender:remove-background: [epoch 043] average training loss: 3713.9666 cellbender:remove-background: [epoch 044] average training loss: 3727.0354 cellbender:remove-background: [epoch 045] average training loss: 3748.3187 cellbender:remove-background: [epoch 045] average test loss: 3734.2708 cellbender:remove-background: [epoch 046] average training loss: 3752.4969 cellbender:remove-background: [epoch 047] average training loss: 3764.3692 cellbender:remove-background: [epoch 048] average training loss: 3781.4591 cellbender:remove-background: [epoch 049] average training loss: 3781.7830 cellbender:remove-background: [epoch 050] average training loss: 3813.0160 cellbender:remove-background: [epoch 050] average test loss: 3718.1056 cellbender:remove-background: [epoch 051] average training loss: 3806.0603 cellbender:remove-background: [epoch 052] average training loss: 3831.0049 cellbender:remove-background: [epoch 053] average training loss: 3816.7101 cellbender:remove-background: [epoch 054] average training loss: 3848.2233 cellbender:remove-background: [epoch 055] average training loss: 3832.4677 cellbender:remove-background: [epoch 055] average test loss: 3807.0145 cellbender:remove-background: [epoch 056] average training loss: 3849.8204 cellbender:remove-background: [epoch 057] average training loss: 3855.9642 cellbender:remove-background: [epoch 058] average training loss: 3865.3722 cellbender:remove-background: [epoch 059] average training loss: 3854.3082 cellbender:remove-background: [epoch 060] average training loss: 3841.0809 cellbender:remove-background: [epoch 060] average test loss: 3842.8546 cellbender:remove-background: [epoch 061] average training loss: 3880.1865 cellbender:remove-background: [epoch 062] average training loss: 3878.6663 cellbender:remove-background: [epoch 063] average training loss: 3889.3038 cellbender:remove-background: [epoch 064] average training loss: 3868.5254 cellbender:remove-background: [epoch 065] average training loss: 3876.7113 cellbender:remove-background: [epoch 065] average test loss: 3874.4456 cellbender:remove-background: [epoch 066] average training loss: 3865.7655 cellbender:remove-background: [epoch 067] average training loss: 3869.5621 cellbender:remove-background: [epoch 068] average training loss: 3862.8942 cellbender:remove-background: [epoch 069] average training loss: 3893.8645 cellbender:remove-background: [epoch 070] average training loss: 3880.4136 cellbender:remove-background: [epoch 070] average test loss: 3917.5492 cellbender:remove-background: [epoch 071] average training loss: 3909.5903 cellbender:remove-background: [epoch 072] average training loss: 3879.9018 cellbender:remove-background: [epoch 073] average training loss: 3888.2104 cellbender:remove-background: [epoch 074] average training loss: 3894.2028 cellbender:remove-background: [epoch 075] average training loss: 3939.8342 cellbender:remove-background: [epoch 075] average test loss: 4006.4346 cellbender:remove-background: [epoch 076] average training loss: 3931.7390 cellbender:remove-background: [epoch 077] average training loss: 3909.5110 cellbender:remove-background: [epoch 078] average training loss: 3879.2489 cellbender:remove-background: [epoch 079] average training loss: 3897.2358 cellbender:remove-background: [epoch 080] average training loss: 3894.0232 cellbender:remove-background: [epoch 080] average test loss: 3924.6137 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/2765-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 081] average training loss: 3908.7115 cellbender:remove-background: [epoch 082] average training loss: 3899.7137 cellbender:remove-background: [epoch 083] average training loss: 3892.6852 cellbender:remove-background: [epoch 084] average training loss: 3923.1703 cellbender:remove-background: [epoch 085] average training loss: 3874.7721 cellbender:remove-background: [epoch 085] average test loss: 3901.4625 cellbender:remove-background: [epoch 086] average training loss: 3875.3650 cellbender:remove-background: [epoch 087] average training loss: 3911.4501 cellbender:remove-background: [epoch 088] average training loss: 3905.6955 cellbender:remove-background: [epoch 089] average training loss: 3871.7453 cellbender:remove-background: [epoch 090] average training loss: 3890.2644 cellbender:remove-background: [epoch 090] average test loss: 3992.0428 cellbender:remove-background: [epoch 091] average training loss: 3910.7797 cellbender:remove-background: [epoch 092] average training loss: 3876.6005 cellbender:remove-background: [epoch 093] average training loss: 3869.7091 cellbender:remove-background: [epoch 094] average training loss: 3889.9565 cellbender:remove-background: [epoch 095] average training loss: 3911.3613 cellbender:remove-background: [epoch 095] average test loss: 3875.9866 cellbender:remove-background: [epoch 096] average training loss: 3910.4408 cellbender:remove-background: [epoch 097] average training loss: 3889.6774 cellbender:remove-background: [epoch 098] average training loss: 3879.5807 cellbender:remove-background: [epoch 099] average training loss: 3928.7275 cellbender:remove-background: [epoch 100] average training loss: 3911.2098 cellbender:remove-background: [epoch 100] average test loss: 3952.7618 cellbender:remove-background: [epoch 101] average training loss: 3902.7164 cellbender:remove-background: [epoch 102] average training loss: 3886.5852 cellbender:remove-background: [epoch 103] average training loss: 3881.9166 cellbender:remove-background: [epoch 104] average training loss: 3862.8069 cellbender:remove-background: [epoch 105] average training loss: 3921.3638 cellbender:remove-background: [epoch 105] average test loss: 3941.9301 cellbender:remove-background: [epoch 106] average training loss: 3905.7866 cellbender:remove-background: [epoch 107] average training loss: 3893.0903 cellbender:remove-background: [epoch 108] average training loss: 3858.4536 cellbender:remove-background: [epoch 109] average training loss: 3914.8335 cellbender:remove-background: [epoch 110] average training loss: 3876.2312 cellbender:remove-background: [epoch 110] average test loss: 3881.0147 cellbender:remove-background: [epoch 111] average training loss: 3892.7947 cellbender:remove-background: [epoch 112] average training loss: 3923.3331 cellbender:remove-background: [epoch 113] average training loss: 3892.6746 cellbender:remove-background: [epoch 114] average training loss: 3920.2472 cellbender:remove-background: [epoch 115] average training loss: 3913.5939 cellbender:remove-background: [epoch 115] average test loss: 4007.7148 cellbender:remove-background: [epoch 116] average training loss: 3903.9336 cellbender:remove-background: [epoch 117] average training loss: 3898.5409 cellbender:remove-background: [epoch 118] average training loss: 3912.1903 cellbender:remove-background: [epoch 119] average training loss: 3893.8610 cellbender:remove-background: [epoch 120] average training loss: 3873.2361 cellbender:remove-background: [epoch 120] average test loss: 3910.4515 cellbender:remove-background: [epoch 121] average training loss: 3902.1622 cellbender:remove-background: [epoch 122] average training loss: 3880.3810 cellbender:remove-background: [epoch 123] average training loss: 3908.8646 cellbender:remove-background: [epoch 124] average training loss: 3878.8391 cellbender:remove-background: [epoch 125] average training loss: 3936.2705 cellbender:remove-background: [epoch 125] average test loss: 3871.1952 cellbender:remove-background: [epoch 126] average training loss: 3866.6928 cellbender:remove-background: [epoch 127] average training loss: 3890.0746 cellbender:remove-background: [epoch 128] average training loss: 3878.7764 cellbender:remove-background: [epoch 129] average training loss: 3955.6625 cellbender:remove-background: [epoch 130] average training loss: 3891.5960 cellbender:remove-background: [epoch 130] average test loss: 3886.8446 cellbender:remove-background: [epoch 131] average training loss: 3877.8460 cellbender:remove-background: [epoch 132] average training loss: 3884.3448 cellbender:remove-background: [epoch 133] average training loss: 3894.7174 cellbender:remove-background: [epoch 134] average training loss: 3840.1695 cellbender:remove-background: [epoch 135] average training loss: 3886.7880 cellbender:remove-background: [epoch 135] average test loss: 3983.1275 cellbender:remove-background: [epoch 136] average training loss: 3874.3680 cellbender:remove-background: [epoch 137] average training loss: 3889.8715 cellbender:remove-background: [epoch 138] average training loss: 3885.2800 cellbender:remove-background: [epoch 139] average training loss: 3884.0116 cellbender:remove-background: [epoch 140] average training loss: 3880.1462 cellbender:remove-background: [epoch 140] average test loss: 3913.0005 cellbender:remove-background: [epoch 141] average training loss: 3852.0611 cellbender:remove-background: [epoch 142] average training loss: 3875.4077 cellbender:remove-background: [epoch 143] average training loss: 3887.7001 cellbender:remove-background: [epoch 144] average training loss: 3887.5228 cellbender:remove-background: [epoch 145] average training loss: 3880.4574 cellbender:remove-background: [epoch 145] average test loss: 3966.6381 cellbender:remove-background: [epoch 146] average training loss: 3874.6428 cellbender:remove-background: [epoch 147] average training loss: 3868.9234 cellbender:remove-background: [epoch 148] average training loss: 3880.1559 cellbender:remove-background: [epoch 149] average training loss: 3873.0897 cellbender:remove-background: [epoch 150] average training loss: 3878.1117 cellbender:remove-background: [epoch 150] average test loss: 4028.6359 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/2765-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:47:10 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp3z8puymh cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp3z8puymh /tmp/tmp3z8puymh/d085eba2f8_random.pyro /tmp/tmp3z8puymh/d085eba2f8_random.cuda /tmp/tmp3z8puymh/d085eba2f8_model.torch /tmp/tmp3z8puymh/d085eba2f8_optim.torch /tmp/tmp3z8puymh/d085eba2f8_optim.pyro /tmp/tmp3z8puymh/d085eba2f8_params.pyro /tmp/tmp3z8puymh/d085eba2f8_train.loaderstate /tmp/tmp3z8puymh/d085eba2f8_test.loaderstate /tmp/tmp3z8puymh/d085eba2f8_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 (1/156) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/156) cellbender:remove-background: Working on chunk (3/156) cellbender:remove-background: Working on chunk (4/156) cellbender:remove-background: Working on chunk (5/156) cellbender:remove-background: Working on chunk (6/156) cellbender:remove-background: Working on chunk (7/156) cellbender:remove-background: Working on chunk (8/156) cellbender:remove-background: Working on chunk (9/156) cellbender:remove-background: Working on chunk (10/156) cellbender:remove-background: Working on chunk (11/156) cellbender:remove-background: Working on chunk (12/156) cellbender:remove-background: Working on chunk (13/156) cellbender:remove-background: Working on chunk (14/156) cellbender:remove-background: Working on chunk (15/156) cellbender:remove-background: Working on chunk (16/156) cellbender:remove-background: 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cellbender:remove-background: Working on chunk (141/156) cellbender:remove-background: Working on chunk (142/156) cellbender:remove-background: Working on chunk (143/156) cellbender:remove-background: Working on chunk (144/156) cellbender:remove-background: Working on chunk (145/156) cellbender:remove-background: Working on chunk (146/156) cellbender:remove-background: Working on chunk (147/156) cellbender:remove-background: Working on chunk (148/156) cellbender:remove-background: Working on chunk (149/156) cellbender:remove-background: Working on chunk (150/156) cellbender:remove-background: Working on chunk (151/156) cellbender:remove-background: Working on chunk (152/156) cellbender:remove-background: Working on chunk (153/156) cellbender:remove-background: Working on chunk (154/156) cellbender:remove-background: Working on chunk (155/156) cellbender:remove-background: Working on chunk (156/156) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-Hippocampus/2765-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/2765-Schizophrenia-Hippocampus/2765-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:53:17 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2765-Schizophrenia-Hippocampus/2765-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/2765-Schizophrenia-Hippocampus/2765-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: [1.78 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 16:06:21 Total MCKP estimation time = 754.45 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/2765-Schizophrenia-Hippocampus/2765-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/2765-Schizophrenia-Hippocampus/2765-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/2765-Schizophrenia-Hippocampus/2765-Schizophrenia-Hippocampus.cellbender.output_metrics.csv Traceback (most recent call last): File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in 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 ) 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 from nbconvert.nbconvertapp import main File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in from .exporters import * File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in from .asciidoc import ASCIIDocExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in from .templateexporter import TemplateExporter File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in 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 ) 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/2765-Schizophrenia-Hippocampus/2765-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:06:41