cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1601-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1601-Bipolar-Hippocampus/1601-Bipolar-Hippocampus.cellbender.output.h5 --cuda --expected-cells 10650 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 7886efd2e7) cellbender:remove-background: 2024-06-06 16:24:19 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/1601-Bipolar-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: 32016 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 4742 cellbender:remove-background: Prior on counts for empty droplets is 341 cellbender:remove-background: Excluding 9318 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 22698 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 170 cellbender:remove-background: Using 10650 probable cell barcodes, plus an additional 9350 barcodes, and 14368 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 335 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpz7rt43r7 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpz7rt43r7 /tmp/tmpz7rt43r7/7886efd2e7_random.pyro /tmp/tmpz7rt43r7/7886efd2e7_random.cuda /tmp/tmpz7rt43r7/7886efd2e7_model.torch /tmp/tmpz7rt43r7/7886efd2e7_optim.torch /tmp/tmpz7rt43r7/7886efd2e7_optim.pyro /tmp/tmpz7rt43r7/7886efd2e7_params.pyro /tmp/tmpz7rt43r7/7886efd2e7_train.loaderstate /tmp/tmpz7rt43r7/7886efd2e7_test.loaderstate /tmp/tmpz7rt43r7/7886efd2e7_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 061] average training loss: 4351.3225 cellbender:remove-background: [epoch 062] average training loss: 4392.2538 (15.5 seconds per epoch) cellbender:remove-background: Will checkpoint every 28 epochs cellbender:remove-background: [epoch 063] average training loss: 4408.3393 cellbender:remove-background: [epoch 064] average training loss: 4435.6596 cellbender:remove-background: [epoch 065] average training loss: 4414.2859 cellbender:remove-background: [epoch 065] average test loss: 4370.2771 cellbender:remove-background: [epoch 066] average training loss: 4449.4496 cellbender:remove-background: [epoch 067] average training loss: 4449.8398 cellbender:remove-background: [epoch 068] average training loss: 4468.0328 cellbender:remove-background: [epoch 069] average training loss: 4441.7659 cellbender:remove-background: [epoch 070] average training loss: 4507.9378 cellbender:remove-background: [epoch 070] average test loss: 4662.2268 cellbender:remove-background: [epoch 071] average training loss: 4500.7723 cellbender:remove-background: [epoch 072] average training loss: 4509.9913 cellbender:remove-background: [epoch 073] average training loss: 4507.1054 cellbender:remove-background: [epoch 074] average training loss: 4546.5487 cellbender:remove-background: [epoch 075] average training loss: 4555.5076 cellbender:remove-background: [epoch 075] average test loss: 4508.4760 cellbender:remove-background: [epoch 076] average training loss: 4539.1176 cellbender:remove-background: [epoch 077] average training loss: 4561.4443 cellbender:remove-background: [epoch 078] average training loss: 4519.7170 cellbender:remove-background: [epoch 079] average training loss: 4514.1926 cellbender:remove-background: [epoch 080] average training loss: 4501.1744 cellbender:remove-background: [epoch 080] average test loss: 4400.4087 cellbender:remove-background: [epoch 081] average training loss: 4471.1918 cellbender:remove-background: [epoch 082] average training loss: 4526.6925 cellbender:remove-background: [epoch 083] average training loss: 4500.7312 cellbender:remove-background: [epoch 084] average training loss: 4496.5842 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/1601-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 085] average training loss: 4507.3125 cellbender:remove-background: [epoch 085] average test loss: 4466.8667 cellbender:remove-background: [epoch 086] average training loss: 4520.3929 cellbender:remove-background: [epoch 087] average training loss: 4534.3762 cellbender:remove-background: [epoch 088] average training loss: 4520.4315 cellbender:remove-background: [epoch 089] average training loss: 4506.7852 cellbender:remove-background: [epoch 090] average training loss: 4516.3622 cellbender:remove-background: [epoch 090] average test loss: 4475.7468 cellbender:remove-background: [epoch 091] average training loss: 4533.8507 cellbender:remove-background: [epoch 092] average training loss: 4482.6696 cellbender:remove-background: [epoch 093] average training loss: 4496.0631 cellbender:remove-background: [epoch 094] average training loss: 4457.7490 cellbender:remove-background: [epoch 095] average training loss: 4493.0986 cellbender:remove-background: [epoch 095] average test loss: 4578.8586 cellbender:remove-background: [epoch 096] average training loss: 4478.7003 cellbender:remove-background: [epoch 097] average training loss: 4499.9356 cellbender:remove-background: [epoch 098] average training loss: 4479.8863 cellbender:remove-background: [epoch 099] average training loss: 4487.4653 cellbender:remove-background: [epoch 100] average training loss: 4483.0722 cellbender:remove-background: [epoch 100] average test loss: 4484.0280 cellbender:remove-background: [epoch 101] average training loss: 4474.0013 cellbender:remove-background: [epoch 102] average training loss: 4506.1889 cellbender:remove-background: [epoch 103] average training loss: 4478.3925 cellbender:remove-background: [epoch 104] average training loss: 4478.7808 cellbender:remove-background: [epoch 105] average training loss: 4471.0056 cellbender:remove-background: [epoch 105] average test loss: 4608.6381 cellbender:remove-background: [epoch 106] average training loss: 4492.7457 cellbender:remove-background: [epoch 107] average training loss: 4474.5619 cellbender:remove-background: [epoch 108] average training loss: 4514.5839 cellbender:remove-background: [epoch 109] average training loss: 4473.5640 cellbender:remove-background: [epoch 110] average training loss: 4457.7706 cellbender:remove-background: [epoch 110] average test loss: 4458.6776 cellbender:remove-background: [epoch 111] average training loss: 4475.7365 cellbender:remove-background: [epoch 112] average training loss: 4476.9464 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/1601-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 113] average training loss: 4507.3876 cellbender:remove-background: [epoch 114] average training loss: 4479.7669 cellbender:remove-background: [epoch 115] average training loss: 4464.9778 cellbender:remove-background: [epoch 115] average test loss: 4479.9092 cellbender:remove-background: [epoch 116] average training loss: 4473.2767 cellbender:remove-background: [epoch 117] average training loss: 4458.1535 cellbender:remove-background: [epoch 118] average training loss: 4450.8112 cellbender:remove-background: [epoch 119] average training loss: 4448.5547 cellbender:remove-background: [epoch 120] average training loss: 4453.4410 cellbender:remove-background: [epoch 120] average test loss: 4536.1527 cellbender:remove-background: [epoch 121] average training loss: 4444.2004 cellbender:remove-background: [epoch 122] average training loss: 4443.6601 cellbender:remove-background: [epoch 123] average training loss: 4466.4045 cellbender:remove-background: [epoch 124] average training loss: 4433.9888 cellbender:remove-background: [epoch 125] average training loss: 4459.3861 cellbender:remove-background: [epoch 125] average test loss: 4437.8254 cellbender:remove-background: [epoch 126] average training loss: 4430.5734 cellbender:remove-background: [epoch 127] average training loss: 4444.0349 cellbender:remove-background: [epoch 128] average training loss: 4450.7901 cellbender:remove-background: [epoch 129] average training loss: 4437.1661 cellbender:remove-background: [epoch 130] average training loss: 4443.4307 cellbender:remove-background: [epoch 130] average test loss: 4416.3915 cellbender:remove-background: [epoch 131] average training loss: 4427.2292 cellbender:remove-background: [epoch 132] average training loss: 4423.5611 cellbender:remove-background: [epoch 133] average training loss: 4425.1394 cellbender:remove-background: [epoch 134] average training loss: 4424.3882 cellbender:remove-background: [epoch 135] average training loss: 4431.1747 cellbender:remove-background: [epoch 135] average test loss: 4455.4419 cellbender:remove-background: [epoch 136] average training loss: 4428.2084 cellbender:remove-background: [epoch 137] average training loss: 4429.3297 cellbender:remove-background: [epoch 138] average training loss: 4444.6995 cellbender:remove-background: [epoch 139] average training loss: 4451.0632 cellbender:remove-background: [epoch 140] average training loss: 4412.8346 cellbender:remove-background: [epoch 140] average test loss: 4458.1324 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/1601-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 141] average training loss: 4450.1270 cellbender:remove-background: [epoch 142] average training loss: 4425.6760 cellbender:remove-background: [epoch 143] average training loss: 4432.7770 cellbender:remove-background: [epoch 144] average training loss: 4432.7931 cellbender:remove-background: [epoch 145] average training loss: 4420.8310 cellbender:remove-background: [epoch 145] average test loss: 4463.5590 cellbender:remove-background: [epoch 146] average training loss: 4448.4272 cellbender:remove-background: [epoch 147] average training loss: 4438.7179 cellbender:remove-background: [epoch 148] average training loss: 4424.4960 cellbender:remove-background: [epoch 149] average training loss: 4416.6165 cellbender:remove-background: [epoch 150] average training loss: 4415.8714 cellbender:remove-background: [epoch 150] average test loss: 4442.7254 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/1601-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 16:57:37 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmplf2mz9zq cellbender:remove-background: Successfully unpacked tarball to /tmp/tmplf2mz9zq /tmp/tmplf2mz9zq/7886efd2e7_random.pyro /tmp/tmplf2mz9zq/7886efd2e7_random.cuda /tmp/tmplf2mz9zq/7886efd2e7_model.torch /tmp/tmplf2mz9zq/7886efd2e7_optim.torch /tmp/tmplf2mz9zq/7886efd2e7_optim.pyro /tmp/tmplf2mz9zq/7886efd2e7_params.pyro /tmp/tmplf2mz9zq/7886efd2e7_train.loaderstate /tmp/tmplf2mz9zq/7886efd2e7_test.loaderstate /tmp/tmplf2mz9zq/7886efd2e7_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 (1/139) cellbender:remove-background: [0.06 mins per chunk] cellbender:remove-background: Working on chunk (2/139) cellbender:remove-background: Working on chunk (3/139) cellbender:remove-background: Working on chunk (4/139) cellbender:remove-background: Working on chunk (5/139) cellbender:remove-background: Working on chunk (6/139) cellbender:remove-background: Working on chunk (7/139) 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cellbender:remove-background: Working on chunk (114/139) cellbender:remove-background: Working on chunk (115/139) cellbender:remove-background: Working on chunk (116/139) cellbender:remove-background: Working on chunk (117/139) cellbender:remove-background: Working on chunk (118/139) cellbender:remove-background: Working on chunk (119/139) cellbender:remove-background: Working on chunk (120/139) cellbender:remove-background: Working on chunk (121/139) cellbender:remove-background: Working on chunk (122/139) cellbender:remove-background: Working on chunk (123/139) cellbender:remove-background: Working on chunk (124/139) cellbender:remove-background: Working on chunk (125/139) cellbender:remove-background: Working on chunk (126/139) cellbender:remove-background: Working on chunk (127/139) cellbender:remove-background: Working on chunk (128/139) cellbender:remove-background: Working on chunk (129/139) cellbender:remove-background: Working on chunk (130/139) cellbender:remove-background: Working on chunk (131/139) cellbender:remove-background: Working on chunk (132/139) cellbender:remove-background: Working on chunk (133/139) cellbender:remove-background: Working on chunk (134/139) cellbender:remove-background: Working on chunk (135/139) cellbender:remove-background: Working on chunk (136/139) cellbender:remove-background: Working on chunk (137/139) cellbender:remove-background: Working on chunk (138/139) cellbender:remove-background: Working on chunk (139/139) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1601-Bipolar-Hippocampus/1601-Bipolar-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/1601-Bipolar-Hippocampus/1601-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 17:09:57 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1601-Bipolar-Hippocampus/1601-Bipolar-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1601-Bipolar-Hippocampus/1601-Bipolar-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: [2.95 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 17:32:49 Total MCKP estimation time = 1296.40 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/1601-Bipolar-Hippocampus/1601-Bipolar-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/1601-Bipolar-Hippocampus/1601-Bipolar-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/1601-Bipolar-Hippocampus/1601-Bipolar-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/1601-Bipolar-Hippocampus/1601-Bipolar-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 17:33:40