cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1317-Bipolar-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1317-Bipolar-Hippocampus/1317-Bipolar-Hippocampus.cellbender.output.h5 --cuda --expected-cells 6699 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 524a2afc83) cellbender:remove-background: 2024-06-06 14:54:29 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/1317-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: 30697 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 372 cellbender:remove-background: Prior on counts for empty droplets is 32 cellbender:remove-background: Excluding 8039 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 22658 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 16 cellbender:remove-background: Using 6699 probable cell barcodes, plus an additional 13301 barcodes, and 36522 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 31 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpf2wbkw2h 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: 1261.3033 cellbender:remove-background: [epoch 002] average training loss: 1109.0370 (6.3 seconds per epoch) cellbender:remove-background: Will checkpoint every 67 epochs cellbender:remove-background: [epoch 003] average training loss: 1024.7224 cellbender:remove-background: [epoch 004] average training loss: 988.5629 cellbender:remove-background: [epoch 005] average training loss: 975.4821 cellbender:remove-background: [epoch 005] average test loss: 1013.6470 cellbender:remove-background: [epoch 006] average training loss: 969.2502 cellbender:remove-background: [epoch 007] average training loss: 956.9769 cellbender:remove-background: [epoch 008] average training loss: 957.6137 cellbender:remove-background: [epoch 009] average training loss: 956.4467 cellbender:remove-background: [epoch 010] average training loss: 955.2286 cellbender:remove-background: [epoch 010] average test loss: 965.5019 cellbender:remove-background: [epoch 011] average training loss: 950.6141 cellbender:remove-background: [epoch 012] average training loss: 954.1418 cellbender:remove-background: [epoch 013] average training loss: 945.5752 cellbender:remove-background: [epoch 014] average training loss: 943.2820 cellbender:remove-background: [epoch 015] average training loss: 911.9611 cellbender:remove-background: [epoch 015] average test loss: 929.2018 cellbender:remove-background: [epoch 016] average training loss: 895.6519 cellbender:remove-background: [epoch 017] average training loss: 875.8562 cellbender:remove-background: [epoch 018] average training loss: 868.8864 cellbender:remove-background: [epoch 019] average training loss: 864.6832 cellbender:remove-background: [epoch 020] average training loss: 861.3256 cellbender:remove-background: [epoch 020] average test loss: 884.9760 cellbender:remove-background: [epoch 021] average training loss: 857.7388 cellbender:remove-background: [epoch 022] average training loss: 855.2869 cellbender:remove-background: [epoch 023] average training loss: 853.7159 cellbender:remove-background: [epoch 024] average training loss: 852.9858 cellbender:remove-background: [epoch 025] average training loss: 852.9116 cellbender:remove-background: [epoch 025] average test loss: 868.2384 cellbender:remove-background: [epoch 026] average training loss: 850.5548 cellbender:remove-background: [epoch 027] average training loss: 850.3518 cellbender:remove-background: [epoch 028] average training loss: 849.5085 cellbender:remove-background: [epoch 029] average training loss: 849.1198 cellbender:remove-background: [epoch 030] average training loss: 849.3048 cellbender:remove-background: [epoch 030] average test loss: 876.1150 cellbender:remove-background: [epoch 031] average training loss: 848.2166 cellbender:remove-background: [epoch 032] average training loss: 848.6860 cellbender:remove-background: [epoch 033] average training loss: 848.5819 cellbender:remove-background: [epoch 034] average training loss: 848.2523 cellbender:remove-background: [epoch 035] average training loss: 848.3878 cellbender:remove-background: [epoch 035] average test loss: 874.4177 cellbender:remove-background: [epoch 036] average training loss: 848.2312 cellbender:remove-background: [epoch 037] average training loss: 847.3133 cellbender:remove-background: [epoch 038] average training loss: 847.8056 cellbender:remove-background: [epoch 039] average training loss: 847.0548 cellbender:remove-background: [epoch 040] average training loss: 846.5172 cellbender:remove-background: [epoch 040] average test loss: 868.4579 cellbender:remove-background: [epoch 041] average training loss: 846.1734 cellbender:remove-background: [epoch 042] average training loss: 846.2577 cellbender:remove-background: [epoch 043] average training loss: 846.3600 cellbender:remove-background: [epoch 044] average training loss: 845.9520 cellbender:remove-background: [epoch 045] average training loss: 845.2439 cellbender:remove-background: [epoch 045] average test loss: 869.4987 cellbender:remove-background: [epoch 046] average training loss: 845.1343 cellbender:remove-background: [epoch 047] average training loss: 843.4501 cellbender:remove-background: [epoch 048] average training loss: 844.9235 cellbender:remove-background: [epoch 049] average training loss: 844.9147 cellbender:remove-background: [epoch 050] average training loss: 844.3851 cellbender:remove-background: [epoch 050] average test loss: 859.4516 cellbender:remove-background: [epoch 051] average training loss: 844.1002 cellbender:remove-background: [epoch 052] average training loss: 842.5759 cellbender:remove-background: [epoch 053] average training loss: 839.9706 cellbender:remove-background: [epoch 054] average training loss: 843.0492 cellbender:remove-background: [epoch 055] average training loss: 839.2562 cellbender:remove-background: [epoch 055] average test loss: 863.9803 cellbender:remove-background: [epoch 056] average training loss: 843.9125 cellbender:remove-background: [epoch 057] average training loss: 842.6444 cellbender:remove-background: [epoch 058] average training loss: 845.3144 cellbender:remove-background: [epoch 059] average training loss: 841.9715 cellbender:remove-background: [epoch 060] average training loss: 844.5396 cellbender:remove-background: [epoch 060] average test loss: 861.9564 cellbender:remove-background: [epoch 061] average training loss: 845.3443 cellbender:remove-background: [epoch 062] average training loss: 841.2560 cellbender:remove-background: [epoch 063] average training loss: 838.1457 cellbender:remove-background: [epoch 064] average training loss: 837.6555 cellbender:remove-background: [epoch 065] average training loss: 840.2539 cellbender:remove-background: [epoch 065] average test loss: 864.9048 cellbender:remove-background: [epoch 066] average training loss: 842.4108 cellbender:remove-background: [epoch 067] average training loss: 837.9643 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/1317-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 068] average training loss: 842.1615 cellbender:remove-background: [epoch 069] average training loss: 836.3743 cellbender:remove-background: [epoch 070] average training loss: 840.7936 cellbender:remove-background: [epoch 070] average test loss: 867.1111 cellbender:remove-background: [epoch 071] average training loss: 839.6823 cellbender:remove-background: [epoch 072] average training loss: 837.5447 cellbender:remove-background: [epoch 073] average training loss: 843.2509 cellbender:remove-background: [epoch 074] average training loss: 840.4651 cellbender:remove-background: [epoch 075] average training loss: 839.3682 cellbender:remove-background: [epoch 075] average test loss: 877.1172 cellbender:remove-background: [epoch 076] average training loss: 842.6924 cellbender:remove-background: [epoch 077] average training loss: 839.0709 cellbender:remove-background: [epoch 078] average training loss: 839.8277 cellbender:remove-background: [epoch 079] average training loss: 844.1182 cellbender:remove-background: [epoch 080] average training loss: 841.8914 cellbender:remove-background: [epoch 080] average test loss: 879.2252 cellbender:remove-background: [epoch 081] average training loss: 842.4816 cellbender:remove-background: [epoch 082] average training loss: 844.3240 cellbender:remove-background: [epoch 083] average training loss: 840.3672 cellbender:remove-background: [epoch 084] average training loss: 840.9117 cellbender:remove-background: [epoch 085] average training loss: 837.0021 cellbender:remove-background: [epoch 085] average test loss: 871.9190 cellbender:remove-background: [epoch 086] average training loss: 837.0887 cellbender:remove-background: [epoch 087] average training loss: 841.1368 cellbender:remove-background: [epoch 088] average training loss: 838.0571 cellbender:remove-background: [epoch 089] average training loss: 839.1081 cellbender:remove-background: [epoch 090] average training loss: 835.5789 cellbender:remove-background: [epoch 090] average test loss: 870.3978 cellbender:remove-background: [epoch 091] average training loss: 835.5860 cellbender:remove-background: [epoch 092] average training loss: 834.8992 cellbender:remove-background: [epoch 093] average training loss: 831.9727 cellbender:remove-background: [epoch 094] average training loss: 834.8303 cellbender:remove-background: [epoch 095] average training loss: 833.9282 cellbender:remove-background: [epoch 095] average test loss: 880.5737 cellbender:remove-background: [epoch 096] average training loss: 834.0900 cellbender:remove-background: [epoch 097] average training loss: 834.5018 cellbender:remove-background: [epoch 098] average training loss: 833.2787 cellbender:remove-background: [epoch 099] average training loss: 833.0445 cellbender:remove-background: [epoch 100] average training loss: 832.9848 cellbender:remove-background: [epoch 100] average test loss: 870.7772 cellbender:remove-background: [epoch 101] average training loss: 832.3603 cellbender:remove-background: [epoch 102] average training loss: 833.2950 cellbender:remove-background: [epoch 103] average training loss: 832.6632 cellbender:remove-background: [epoch 104] average training loss: 833.2235 cellbender:remove-background: [epoch 105] average training loss: 829.2375 cellbender:remove-background: [epoch 105] average test loss: 876.1244 cellbender:remove-background: [epoch 106] average training loss: 832.6311 cellbender:remove-background: [epoch 107] average training loss: 829.6377 cellbender:remove-background: [epoch 108] average training loss: 831.9164 cellbender:remove-background: [epoch 109] average training loss: 830.6696 cellbender:remove-background: [epoch 110] average training loss: 828.8338 cellbender:remove-background: [epoch 110] average test loss: 881.3773 cellbender:remove-background: [epoch 111] average training loss: 830.8113 cellbender:remove-background: [epoch 112] average training loss: 830.3095 cellbender:remove-background: [epoch 113] average training loss: 830.8170 cellbender:remove-background: [epoch 114] average training loss: 829.9202 cellbender:remove-background: [epoch 115] average training loss: 828.0948 cellbender:remove-background: [epoch 115] average test loss: 877.7262 cellbender:remove-background: [epoch 116] average training loss: 829.8028 cellbender:remove-background: [epoch 117] average training loss: 827.2057 cellbender:remove-background: [epoch 118] average training loss: 829.1296 cellbender:remove-background: [epoch 119] average training loss: 829.0491 cellbender:remove-background: [epoch 120] average training loss: 826.9249 cellbender:remove-background: [epoch 120] average test loss: 874.3522 cellbender:remove-background: [epoch 121] average training loss: 829.7179 cellbender:remove-background: [epoch 122] average training loss: 828.8027 cellbender:remove-background: [epoch 123] average training loss: 827.2112 cellbender:remove-background: [epoch 124] average training loss: 830.0069 cellbender:remove-background: [epoch 125] average training loss: 827.5715 cellbender:remove-background: [epoch 125] average test loss: 880.0681 cellbender:remove-background: [epoch 126] average training loss: 828.1921 cellbender:remove-background: [epoch 127] average training loss: 828.1798 cellbender:remove-background: [epoch 128] average training loss: 830.4245 cellbender:remove-background: [epoch 129] average training loss: 827.7388 cellbender:remove-background: [epoch 130] average training loss: 828.3664 cellbender:remove-background: [epoch 130] average test loss: 879.9579 cellbender:remove-background: [epoch 131] average training loss: 829.7734 cellbender:remove-background: [epoch 132] average training loss: 828.5969 cellbender:remove-background: [epoch 133] average training loss: 826.8252 cellbender:remove-background: [epoch 134] average training loss: 828.0960 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/1317-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 135] average training loss: 828.1065 cellbender:remove-background: [epoch 135] average test loss: 875.7783 cellbender:remove-background: [epoch 136] average training loss: 827.1742 cellbender:remove-background: [epoch 137] average training loss: 827.3576 cellbender:remove-background: [epoch 138] average training loss: 828.9645 cellbender:remove-background: [epoch 139] average training loss: 828.1991 cellbender:remove-background: [epoch 140] average training loss: 827.6435 cellbender:remove-background: [epoch 140] average test loss: 880.7514 cellbender:remove-background: [epoch 141] average training loss: 827.9030 cellbender:remove-background: [epoch 142] average training loss: 826.9398 cellbender:remove-background: [epoch 143] average training loss: 827.8708 cellbender:remove-background: [epoch 144] average training loss: 827.3774 cellbender:remove-background: [epoch 145] average training loss: 827.4919 cellbender:remove-background: [epoch 145] average test loss: 874.9831 cellbender:remove-background: [epoch 146] average training loss: 826.4722 cellbender:remove-background: [epoch 147] average training loss: 827.2736 cellbender:remove-background: [epoch 148] average training loss: 825.9515 cellbender:remove-background: [epoch 149] average training loss: 825.8985 cellbender:remove-background: [epoch 150] average training loss: 827.3871 cellbender:remove-background: [epoch 150] average test loss: 877.5138 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/1317-Bipolar-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:13:35 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp30fqe8hj cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp30fqe8hj /tmp/tmp30fqe8hj/524a2afc83_random.pyro /tmp/tmp30fqe8hj/524a2afc83_random.cuda /tmp/tmp30fqe8hj/524a2afc83_model.torch /tmp/tmp30fqe8hj/524a2afc83_optim.torch /tmp/tmp30fqe8hj/524a2afc83_optim.pyro /tmp/tmp30fqe8hj/524a2afc83_params.pyro /tmp/tmp30fqe8hj/524a2afc83_train.loaderstate /tmp/tmp30fqe8hj/524a2afc83_test.loaderstate /tmp/tmp30fqe8hj/524a2afc83_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 (1/46) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/46) cellbender:remove-background: Working on chunk (3/46) cellbender:remove-background: Working on chunk (4/46) cellbender:remove-background: Working on chunk (5/46) cellbender:remove-background: Working on chunk (6/46) cellbender:remove-background: Working on chunk (7/46) cellbender:remove-background: Working on chunk (8/46) cellbender:remove-background: Working on chunk (9/46) cellbender:remove-background: Working on chunk (10/46) cellbender:remove-background: Working on chunk (11/46) cellbender:remove-background: Working on chunk (12/46) cellbender:remove-background: Working on chunk (13/46) cellbender:remove-background: Working on chunk (14/46) cellbender:remove-background: Working on chunk (15/46) cellbender:remove-background: Working on chunk (16/46) cellbender:remove-background: Working on chunk (17/46) cellbender:remove-background: Working on chunk (18/46) cellbender:remove-background: Working on chunk (19/46) cellbender:remove-background: Working on chunk (20/46) cellbender:remove-background: Working on chunk (21/46) cellbender:remove-background: Working on chunk (22/46) cellbender:remove-background: Working on chunk (23/46) cellbender:remove-background: Working on chunk (24/46) cellbender:remove-background: Working on chunk (25/46) cellbender:remove-background: Working on chunk (26/46) cellbender:remove-background: Working on chunk (27/46) cellbender:remove-background: Working on chunk (28/46) cellbender:remove-background: Working on chunk (29/46) cellbender:remove-background: Working on chunk (30/46) cellbender:remove-background: Working on chunk (31/46) cellbender:remove-background: Working on chunk (32/46) cellbender:remove-background: Working on chunk (33/46) cellbender:remove-background: Working on chunk (34/46) cellbender:remove-background: Working on chunk (35/46) cellbender:remove-background: Working on chunk (36/46) cellbender:remove-background: Working on chunk (37/46) cellbender:remove-background: Working on chunk (38/46) cellbender:remove-background: Working on chunk (39/46) cellbender:remove-background: Working on chunk (40/46) cellbender:remove-background: Working on chunk (41/46) cellbender:remove-background: Working on chunk (42/46) cellbender:remove-background: Working on chunk (43/46) cellbender:remove-background: Working on chunk (44/46) cellbender:remove-background: Working on chunk (45/46) cellbender:remove-background: Working on chunk (46/46) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1317-Bipolar-Hippocampus/1317-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/1317-Bipolar-Hippocampus/1317-Bipolar-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:16:23 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1317-Bipolar-Hippocampus/1317-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/1317-Bipolar-Hippocampus/1317-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: [0.27 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: 2024-06-06 15:18:19 Total MCKP estimation time = 109.31 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/1317-Bipolar-Hippocampus/1317-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/1317-Bipolar-Hippocampus/1317-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/1317-Bipolar-Hippocampus/1317-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/1317-Bipolar-Hippocampus/1317-Bipolar-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:18:26