cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2781-Control-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-Hippocampus/2781-Control-Hippocampus.cellbender.output.h5 --cuda --expected-cells 13111 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 73cdafe65c) cellbender:remove-background: 2024-06-07 16:42:19 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/2781-Control-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: 31060 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2040 cellbender:remove-background: Prior on counts for empty droplets is 207 cellbender:remove-background: Excluding 7490 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 23570 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 103 cellbender:remove-background: Using 13111 probable cell barcodes, plus an additional 6889 barcodes, and 8718 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 201 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpog2c4cse cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpog2c4cse /tmp/tmpog2c4cse/73cdafe65c_random.pyro /tmp/tmpog2c4cse/73cdafe65c_random.cuda /tmp/tmpog2c4cse/73cdafe65c_model.torch /tmp/tmpog2c4cse/73cdafe65c_optim.torch /tmp/tmpog2c4cse/73cdafe65c_optim.pyro /tmp/tmpog2c4cse/73cdafe65c_params.pyro /tmp/tmpog2c4cse/73cdafe65c_train.loaderstate /tmp/tmpog2c4cse/73cdafe65c_test.loaderstate /tmp/tmpog2c4cse/73cdafe65c_args.npy cellbender:remove-background: Loaded partially-trained checkpoint from ckpt.tar.gz cellbender:remove-background: Checkpoint loaded successfully. cellbender:remove-background: Running inference... cellbender:remove-background: [epoch 056] average training loss: 3011.1581 cellbender:remove-background: [epoch 057] average training loss: 3014.5034 (13.5 seconds per epoch) cellbender:remove-background: Will checkpoint every 32 epochs cellbender:remove-background: [epoch 058] average training loss: 3015.8532 cellbender:remove-background: [epoch 059] average training loss: 3013.3345 cellbender:remove-background: [epoch 060] average training loss: 3013.5559 cellbender:remove-background: [epoch 060] average test loss: 3016.3032 cellbender:remove-background: [epoch 061] average training loss: 3016.5846 cellbender:remove-background: [epoch 062] average training loss: 3013.3889 cellbender:remove-background: [epoch 063] average training loss: 3011.3362 cellbender:remove-background: [epoch 064] average training loss: 3013.0800 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/2781-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 065] average training loss: 3010.0801 cellbender:remove-background: [epoch 065] average test loss: 3029.3948 cellbender:remove-background: [epoch 066] average training loss: 3012.6755 cellbender:remove-background: [epoch 067] average training loss: 3011.0873 cellbender:remove-background: [epoch 068] average training loss: 3011.6787 cellbender:remove-background: [epoch 069] average training loss: 3010.7518 cellbender:remove-background: [epoch 070] average training loss: 3005.5338 cellbender:remove-background: [epoch 070] average test loss: 3021.9344 cellbender:remove-background: [epoch 071] average training loss: 3008.9651 cellbender:remove-background: [epoch 072] average training loss: 3007.5015 cellbender:remove-background: [epoch 073] average training loss: 3010.2902 cellbender:remove-background: [epoch 074] average training loss: 3008.7771 cellbender:remove-background: [epoch 075] average training loss: 3005.8067 cellbender:remove-background: [epoch 075] average test loss: 3009.6314 cellbender:remove-background: [epoch 076] average training loss: 3005.3164 cellbender:remove-background: [epoch 077] average training loss: 3005.2868 cellbender:remove-background: [epoch 078] average training loss: 3003.5679 cellbender:remove-background: [epoch 079] average training loss: 3001.0743 cellbender:remove-background: [epoch 080] average training loss: 3000.4778 cellbender:remove-background: [epoch 080] average test loss: 3019.2494 cellbender:remove-background: [epoch 081] average training loss: 3002.4287 cellbender:remove-background: [epoch 082] average training loss: 3001.8564 cellbender:remove-background: [epoch 083] average training loss: 3000.9302 cellbender:remove-background: [epoch 084] average training loss: 2995.8100 cellbender:remove-background: [epoch 085] average training loss: 3001.8338 cellbender:remove-background: [epoch 085] average test loss: 3002.9900 cellbender:remove-background: [epoch 086] average training loss: 2999.0966 cellbender:remove-background: [epoch 087] average training loss: 3000.0059 cellbender:remove-background: [epoch 088] average training loss: 3003.8908 cellbender:remove-background: [epoch 089] average training loss: 3006.4271 cellbender:remove-background: [epoch 090] average training loss: 3006.5797 cellbender:remove-background: [epoch 090] average test loss: 2999.0098 cellbender:remove-background: [epoch 091] average training loss: 3005.6295 cellbender:remove-background: [epoch 092] average training loss: 3004.9397 cellbender:remove-background: [epoch 093] average training loss: 3008.3920 cellbender:remove-background: [epoch 094] average training loss: 3012.4209 cellbender:remove-background: [epoch 095] average training loss: 3009.5142 cellbender:remove-background: [epoch 095] average test loss: 3038.7898 cellbender:remove-background: [epoch 096] average training loss: 3017.8233 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/2781-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 097] average training loss: 3012.6548 cellbender:remove-background: [epoch 098] average training loss: 3007.5840 cellbender:remove-background: [epoch 099] average training loss: 3014.2017 cellbender:remove-background: [epoch 100] average training loss: 3012.1102 cellbender:remove-background: [epoch 100] average test loss: 3018.7133 cellbender:remove-background: [epoch 101] average training loss: 3016.7097 cellbender:remove-background: [epoch 102] average training loss: 3005.2406 cellbender:remove-background: [epoch 103] average training loss: 3009.0286 cellbender:remove-background: [epoch 104] average training loss: 3012.9400 cellbender:remove-background: [epoch 105] average training loss: 3015.4391 cellbender:remove-background: [epoch 105] average test loss: 3049.3678 cellbender:remove-background: [epoch 106] average training loss: 3003.6065 cellbender:remove-background: [epoch 107] average training loss: 3004.4907 cellbender:remove-background: [epoch 108] average training loss: 3019.9593 cellbender:remove-background: [epoch 109] average training loss: 3005.3826 cellbender:remove-background: [epoch 110] average training loss: 3001.8282 cellbender:remove-background: [epoch 110] average test loss: 3026.0837 cellbender:remove-background: [epoch 111] average training loss: 3005.6860 cellbender:remove-background: [epoch 112] average training loss: 2999.0621 cellbender:remove-background: [epoch 113] average training loss: 3013.3410 cellbender:remove-background: [epoch 114] average training loss: 3002.4156 cellbender:remove-background: [epoch 115] average training loss: 2997.2242 cellbender:remove-background: [epoch 115] average test loss: 3020.1131 cellbender:remove-background: [epoch 116] average training loss: 3004.2151 cellbender:remove-background: [epoch 117] average training loss: 3005.5540 cellbender:remove-background: [epoch 118] average training loss: 3002.1703 cellbender:remove-background: [epoch 119] average training loss: 3000.4316 cellbender:remove-background: [epoch 120] average training loss: 2998.0046 cellbender:remove-background: [epoch 120] average test loss: 3041.7450 cellbender:remove-background: [epoch 121] average training loss: 3000.5664 cellbender:remove-background: [epoch 122] average training loss: 3001.8871 cellbender:remove-background: [epoch 123] average training loss: 2997.1193 cellbender:remove-background: [epoch 124] average training loss: 3001.7389 cellbender:remove-background: [epoch 125] average training loss: 2998.5468 cellbender:remove-background: [epoch 125] average test loss: 3026.0716 cellbender:remove-background: [epoch 126] average training loss: 3000.6833 cellbender:remove-background: [epoch 127] average training loss: 2995.4934 cellbender:remove-background: [epoch 128] average training loss: 2998.7255 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/2781-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 129] average training loss: 2998.4490 cellbender:remove-background: [epoch 130] average training loss: 3001.7954 cellbender:remove-background: [epoch 130] average test loss: 3035.6441 cellbender:remove-background: [epoch 131] average training loss: 3001.9300 cellbender:remove-background: [epoch 132] average training loss: 2996.2903 cellbender:remove-background: [epoch 133] average training loss: 3002.5473 cellbender:remove-background: [epoch 134] average training loss: 3000.7662 cellbender:remove-background: [epoch 135] average training loss: 2999.4343 cellbender:remove-background: [epoch 135] average test loss: 3021.2204 cellbender:remove-background: [epoch 136] average training loss: 2999.3212 cellbender:remove-background: [epoch 137] average training loss: 2996.1468 cellbender:remove-background: [epoch 138] average training loss: 2995.2307 cellbender:remove-background: [epoch 139] average training loss: 2999.2715 cellbender:remove-background: [epoch 140] average training loss: 2997.0382 cellbender:remove-background: [epoch 140] average test loss: 3037.5703 cellbender:remove-background: [epoch 141] average training loss: 2998.8456 cellbender:remove-background: [epoch 142] average training loss: 2997.1817 cellbender:remove-background: [epoch 143] average training loss: 2999.7241 cellbender:remove-background: [epoch 144] average training loss: 2995.7597 cellbender:remove-background: [epoch 145] average training loss: 2999.5979 cellbender:remove-background: [epoch 145] average test loss: 3013.4586 cellbender:remove-background: [epoch 146] average training loss: 2998.8195 cellbender:remove-background: [epoch 147] average training loss: 2996.6356 cellbender:remove-background: [epoch 148] average training loss: 2996.0320 cellbender:remove-background: [epoch 149] average training loss: 2997.3344 cellbender:remove-background: [epoch 150] average training loss: 2998.0135 cellbender:remove-background: [epoch 150] average test loss: 3026.6910 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/2781-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-07 17:15:28 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpbrdjnwse cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpbrdjnwse /tmp/tmpbrdjnwse/73cdafe65c_random.pyro /tmp/tmpbrdjnwse/73cdafe65c_random.cuda /tmp/tmpbrdjnwse/73cdafe65c_model.torch /tmp/tmpbrdjnwse/73cdafe65c_optim.torch /tmp/tmpbrdjnwse/73cdafe65c_optim.pyro /tmp/tmpbrdjnwse/73cdafe65c_params.pyro /tmp/tmpbrdjnwse/73cdafe65c_train.loaderstate /tmp/tmpbrdjnwse/73cdafe65c_test.loaderstate /tmp/tmpbrdjnwse/73cdafe65c_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 (1/133) cellbender:remove-background: [0.06 mins per chunk] cellbender:remove-background: Working on chunk (2/133) cellbender:remove-background: Working on chunk (3/133) cellbender:remove-background: Working on chunk (4/133) cellbender:remove-background: Working on chunk (5/133) cellbender:remove-background: Working on chunk (6/133) cellbender:remove-background: Working on chunk (7/133) cellbender:remove-background: Working on chunk (8/133) cellbender:remove-background: Working on chunk (9/133) cellbender:remove-background: Working on chunk (10/133) cellbender:remove-background: Working on chunk (11/133) cellbender:remove-background: Working on chunk (12/133) cellbender:remove-background: Working on chunk (13/133) cellbender:remove-background: Working on chunk (14/133) cellbender:remove-background: Working on chunk (15/133) cellbender:remove-background: Working on chunk (16/133) cellbender:remove-background: Working on chunk (17/133) cellbender:remove-background: Working on 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cellbender:remove-background: Working on chunk (107/133) cellbender:remove-background: Working on chunk (108/133) cellbender:remove-background: Working on chunk (109/133) cellbender:remove-background: Working on chunk (110/133) cellbender:remove-background: Working on chunk (111/133) cellbender:remove-background: Working on chunk (112/133) cellbender:remove-background: Working on chunk (113/133) cellbender:remove-background: Working on chunk (114/133) cellbender:remove-background: Working on chunk (115/133) cellbender:remove-background: Working on chunk (116/133) cellbender:remove-background: Working on chunk (117/133) cellbender:remove-background: Working on chunk (118/133) cellbender:remove-background: Working on chunk (119/133) cellbender:remove-background: Working on chunk (120/133) cellbender:remove-background: Working on chunk (121/133) cellbender:remove-background: Working on chunk (122/133) cellbender:remove-background: Working on chunk (123/133) cellbender:remove-background: Working on chunk (124/133) cellbender:remove-background: Working on chunk (125/133) cellbender:remove-background: Working on chunk (126/133) cellbender:remove-background: Working on chunk (127/133) cellbender:remove-background: Working on chunk (128/133) cellbender:remove-background: Working on chunk (129/133) cellbender:remove-background: Working on chunk (130/133) cellbender:remove-background: Working on chunk (131/133) cellbender:remove-background: Working on chunk (132/133) cellbender:remove-background: Working on chunk (133/133) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-Hippocampus/2781-Control-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/2781-Control-Hippocampus/2781-Control-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-07 17:27:24 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-Hippocampus/2781-Control-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2781-Control-Hippocampus/2781-Control-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: [2.27 mins per chunk] cellbender:remove-background: Working on chunk (2/7) cellbender:remove-background: Working on chunk (3/7) cellbender:remove-background: Working on chunk (4/7) cellbender:remove-background: Working on chunk (5/7) cellbender:remove-background: Working on chunk (6/7) cellbender:remove-background: Working on chunk (7/7) cellbender:remove-background: 2024-06-07 17:44:05 Total MCKP estimation time = 950.87 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/2781-Control-Hippocampus/2781-Control-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/2781-Control-Hippocampus/2781-Control-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/2781-Control-Hippocampus/2781-Control-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/2781-Control-Hippocampus/2781-Control-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-07 17:44:36