cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1511-Bipolar-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1511-Bipolar-dACC/1511-Bipolar-dACC.cellbender.output.h5 --cuda --expected-cells 7289 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 88cf3312fa) cellbender:remove-background: 2024-06-06 15:04:34 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/1511-Bipolar-dACC.raw_feature_bc_matrix.h5 cellbender:remove-background: CellRanger v3 format cellbender:remove-background: Features in dataset: 36601 Gene Expression cellbender:remove-background: Trimming features for inference. cellbender:remove-background: 30214 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 984 cellbender:remove-background: Prior on counts for empty droplets is 57 cellbender:remove-background: Excluding 5738 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 24476 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 28 cellbender:remove-background: Using 7289 probable cell barcodes, plus an additional 12711 barcodes, and 52033 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 57 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpeyus97zx 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: 2071.5604 cellbender:remove-background: [epoch 002] average training loss: 1806.5235 (6.1 seconds per epoch) cellbender:remove-background: Will checkpoint every 69 epochs cellbender:remove-background: [epoch 003] average training loss: 1643.9949 cellbender:remove-background: [epoch 004] average training loss: 1551.3671 cellbender:remove-background: [epoch 005] average training loss: 1509.3110 cellbender:remove-background: [epoch 005] average test loss: 1478.1293 cellbender:remove-background: [epoch 006] average training loss: 1480.7222 cellbender:remove-background: [epoch 007] average training loss: 1470.0573 cellbender:remove-background: [epoch 008] average training loss: 1466.2299 cellbender:remove-background: [epoch 009] average training loss: 1460.7295 cellbender:remove-background: [epoch 010] average training loss: 1457.0096 cellbender:remove-background: [epoch 010] average test loss: 1425.3195 cellbender:remove-background: [epoch 011] average training loss: 1454.9869 cellbender:remove-background: [epoch 012] average training loss: 1455.6578 cellbender:remove-background: [epoch 013] average training loss: 1455.5547 cellbender:remove-background: [epoch 014] average training loss: 1447.9557 cellbender:remove-background: [epoch 015] average training loss: 1419.6082 cellbender:remove-background: [epoch 015] average test loss: 1384.4416 cellbender:remove-background: [epoch 016] average training loss: 1405.5796 cellbender:remove-background: [epoch 017] average training loss: 1406.3495 cellbender:remove-background: [epoch 018] average training loss: 1402.7519 cellbender:remove-background: [epoch 019] average training loss: 1401.3887 cellbender:remove-background: [epoch 020] average training loss: 1399.7659 cellbender:remove-background: [epoch 020] average test loss: 1388.0283 cellbender:remove-background: [epoch 021] average training loss: 1400.0175 cellbender:remove-background: [epoch 022] average training loss: 1399.0588 cellbender:remove-background: [epoch 023] average training loss: 1398.6762 cellbender:remove-background: [epoch 024] average training loss: 1395.8941 cellbender:remove-background: [epoch 025] average training loss: 1395.7367 cellbender:remove-background: [epoch 025] average test loss: 1366.3403 cellbender:remove-background: [epoch 026] average training loss: 1392.8303 cellbender:remove-background: [epoch 027] average training loss: 1392.9463 cellbender:remove-background: [epoch 028] average training loss: 1391.7814 cellbender:remove-background: [epoch 029] average training loss: 1388.1014 cellbender:remove-background: [epoch 030] average training loss: 1385.9460 cellbender:remove-background: [epoch 030] average test loss: 1372.2206 cellbender:remove-background: [epoch 031] average training loss: 1385.6399 cellbender:remove-background: [epoch 032] average training loss: 1384.1541 cellbender:remove-background: [epoch 033] average training loss: 1382.4555 cellbender:remove-background: [epoch 034] average training loss: 1381.8776 cellbender:remove-background: [epoch 035] average training loss: 1379.9576 cellbender:remove-background: [epoch 035] average test loss: 1369.7184 cellbender:remove-background: [epoch 036] average training loss: 1379.1623 cellbender:remove-background: [epoch 037] average training loss: 1377.8481 cellbender:remove-background: [epoch 038] average training loss: 1376.1957 cellbender:remove-background: [epoch 039] average training loss: 1375.3605 cellbender:remove-background: [epoch 040] average training loss: 1374.9395 cellbender:remove-background: [epoch 040] average test loss: 1367.8840 cellbender:remove-background: [epoch 041] average training loss: 1374.3723 cellbender:remove-background: [epoch 042] average training loss: 1383.4756 cellbender:remove-background: [epoch 043] average training loss: 1384.5787 cellbender:remove-background: [epoch 044] average training loss: 1380.0479 cellbender:remove-background: [epoch 045] average training loss: 1377.3817 cellbender:remove-background: [epoch 045] average test loss: 1362.6055 cellbender:remove-background: [epoch 046] average training loss: 1380.0569 cellbender:remove-background: [epoch 047] average training loss: 1384.3473 cellbender:remove-background: [epoch 048] average training loss: 1382.2971 cellbender:remove-background: [epoch 049] average training loss: 1386.4695 cellbender:remove-background: [epoch 050] average training loss: 1386.8811 cellbender:remove-background: [epoch 050] average test loss: 1372.9622 cellbender:remove-background: [epoch 051] average training loss: 1389.9179 cellbender:remove-background: [epoch 052] average training loss: 1395.8237 cellbender:remove-background: [epoch 053] average training loss: 1399.8313 cellbender:remove-background: [epoch 054] average training loss: 1392.1954 cellbender:remove-background: [epoch 055] average training loss: 1394.1924 cellbender:remove-background: [epoch 055] average test loss: 1402.8424 cellbender:remove-background: [epoch 056] average training loss: 1401.7502 cellbender:remove-background: [epoch 057] average training loss: 1401.6963 cellbender:remove-background: [epoch 058] average training loss: 1417.4954 cellbender:remove-background: [epoch 059] average training loss: 1413.2816 cellbender:remove-background: [epoch 060] average training loss: 1415.4924 cellbender:remove-background: [epoch 060] average test loss: 1404.9278 cellbender:remove-background: [epoch 061] average training loss: 1415.1028 cellbender:remove-background: [epoch 062] average training loss: 1414.5261 cellbender:remove-background: [epoch 063] average training loss: 1408.6539 cellbender:remove-background: [epoch 064] average training loss: 1412.3133 cellbender:remove-background: [epoch 065] average training loss: 1408.5836 cellbender:remove-background: [epoch 065] average test loss: 1433.6966 cellbender:remove-background: [epoch 066] average training loss: 1414.7224 cellbender:remove-background: [epoch 067] average training loss: 1417.2745 cellbender:remove-background: [epoch 068] average training loss: 1407.8861 cellbender:remove-background: [epoch 069] average training loss: 1409.1704 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/1511-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 070] average training loss: 1404.1786 cellbender:remove-background: [epoch 070] average test loss: 1393.0324 cellbender:remove-background: [epoch 071] average training loss: 1405.1653 cellbender:remove-background: [epoch 072] average training loss: 1408.3011 cellbender:remove-background: [epoch 073] average training loss: 1407.7300 cellbender:remove-background: [epoch 074] average training loss: 1412.3553 cellbender:remove-background: [epoch 075] average training loss: 1408.3138 cellbender:remove-background: [epoch 075] average test loss: 1407.1461 cellbender:remove-background: [epoch 076] average training loss: 1402.8272 cellbender:remove-background: [epoch 077] average training loss: 1415.6657 cellbender:remove-background: [epoch 078] average training loss: 1412.8279 cellbender:remove-background: [epoch 079] average training loss: 1407.1773 cellbender:remove-background: [epoch 080] average training loss: 1409.0094 cellbender:remove-background: [epoch 080] average test loss: 1402.4282 cellbender:remove-background: [epoch 081] average training loss: 1403.8952 cellbender:remove-background: [epoch 082] average training loss: 1403.3066 cellbender:remove-background: [epoch 083] average training loss: 1403.3249 cellbender:remove-background: [epoch 084] average training loss: 1405.0395 cellbender:remove-background: [epoch 085] average training loss: 1395.5352 cellbender:remove-background: [epoch 085] average test loss: 1405.9835 cellbender:remove-background: [epoch 086] average training loss: 1401.7222 cellbender:remove-background: [epoch 087] average training loss: 1401.0727 cellbender:remove-background: [epoch 088] average training loss: 1397.6633 cellbender:remove-background: [epoch 089] average training loss: 1404.0942 cellbender:remove-background: [epoch 090] average training loss: 1399.6766 cellbender:remove-background: [epoch 090] average test loss: 1420.5697 cellbender:remove-background: [epoch 091] average training loss: 1394.6108 cellbender:remove-background: [epoch 092] average training loss: 1404.5800 cellbender:remove-background: [epoch 093] average training loss: 1399.5327 cellbender:remove-background: [epoch 094] average training loss: 1396.1842 cellbender:remove-background: [epoch 095] average training loss: 1394.9572 cellbender:remove-background: [epoch 095] average test loss: 1442.1954 cellbender:remove-background: [epoch 096] average training loss: 1399.7427 cellbender:remove-background: [epoch 097] average training loss: 1399.8431 cellbender:remove-background: [epoch 098] average training loss: 1395.9979 cellbender:remove-background: [epoch 099] average training loss: 1396.2614 cellbender:remove-background: [epoch 100] average training loss: 1396.3959 cellbender:remove-background: [epoch 100] average test loss: 1409.0556 cellbender:remove-background: [epoch 101] average training loss: 1392.0037 cellbender:remove-background: [epoch 102] average training loss: 1391.8315 cellbender:remove-background: [epoch 103] average training loss: 1392.9560 cellbender:remove-background: [epoch 104] average training loss: 1392.8487 cellbender:remove-background: [epoch 105] average training loss: 1395.0371 cellbender:remove-background: [epoch 105] average test loss: 1410.5585 cellbender:remove-background: [epoch 106] average training loss: 1392.0347 cellbender:remove-background: [epoch 107] average training loss: 1387.6644 cellbender:remove-background: [epoch 108] average training loss: 1391.1415 cellbender:remove-background: [epoch 109] average training loss: 1393.1571 cellbender:remove-background: [epoch 110] average training loss: 1389.6516 cellbender:remove-background: [epoch 110] average test loss: 1407.7650 cellbender:remove-background: [epoch 111] average training loss: 1387.3453 cellbender:remove-background: [epoch 112] average training loss: 1385.5334 cellbender:remove-background: [epoch 113] average training loss: 1386.2441 cellbender:remove-background: [epoch 114] average training loss: 1386.4810 cellbender:remove-background: [epoch 115] average training loss: 1384.3533 cellbender:remove-background: [epoch 115] average test loss: 1400.3202 cellbender:remove-background: [epoch 116] average training loss: 1386.9547 cellbender:remove-background: [epoch 117] average training loss: 1386.1238 cellbender:remove-background: [epoch 118] average training loss: 1385.4781 cellbender:remove-background: [epoch 119] average training loss: 1383.7196 cellbender:remove-background: [epoch 120] average training loss: 1389.2094 cellbender:remove-background: [epoch 120] average test loss: 1403.3749 cellbender:remove-background: [epoch 121] average training loss: 1388.5997 cellbender:remove-background: [epoch 122] average training loss: 1385.1783 cellbender:remove-background: [epoch 123] average training loss: 1385.5350 cellbender:remove-background: [epoch 124] average training loss: 1383.5237 cellbender:remove-background: [epoch 125] average training loss: 1383.9733 cellbender:remove-background: [epoch 125] average test loss: 1398.1720 cellbender:remove-background: [epoch 126] average training loss: 1382.7251 cellbender:remove-background: [epoch 127] average training loss: 1388.1759 cellbender:remove-background: [epoch 128] average training loss: 1385.1024 cellbender:remove-background: [epoch 129] average training loss: 1383.8995 cellbender:remove-background: [epoch 130] average training loss: 1384.1822 cellbender:remove-background: [epoch 130] average test loss: 1416.5033 cellbender:remove-background: [epoch 131] average training loss: 1385.2583 cellbender:remove-background: [epoch 132] average training loss: 1387.2009 cellbender:remove-background: [epoch 133] average training loss: 1385.9246 cellbender:remove-background: [epoch 134] average training loss: 1384.9569 cellbender:remove-background: [epoch 135] average training loss: 1383.4109 cellbender:remove-background: [epoch 135] average test loss: 1405.5278 cellbender:remove-background: [epoch 136] average training loss: 1386.5242 cellbender:remove-background: [epoch 137] average training loss: 1384.0553 cellbender:remove-background: [epoch 138] average training loss: 1385.9566 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/1511-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 139] average training loss: 1385.9042 cellbender:remove-background: [epoch 140] average training loss: 1384.4353 cellbender:remove-background: [epoch 140] average test loss: 1400.7958 cellbender:remove-background: [epoch 141] average training loss: 1384.9335 cellbender:remove-background: [epoch 142] average training loss: 1384.9127 cellbender:remove-background: [epoch 143] average training loss: 1384.6988 cellbender:remove-background: [epoch 144] average training loss: 1383.9075 cellbender:remove-background: [epoch 145] average training loss: 1384.0307 cellbender:remove-background: [epoch 145] average test loss: 1400.9062 cellbender:remove-background: [epoch 146] average training loss: 1383.8633 cellbender:remove-background: [epoch 147] average training loss: 1385.1975 cellbender:remove-background: [epoch 148] average training loss: 1384.4237 cellbender:remove-background: [epoch 149] average training loss: 1383.1985 cellbender:remove-background: [epoch 150] average training loss: 1384.4409 cellbender:remove-background: [epoch 150] average test loss: 1403.3102 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/1511-Bipolar-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:23:27 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpvoimt0fj cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpvoimt0fj /tmp/tmpvoimt0fj/88cf3312fa_random.pyro /tmp/tmpvoimt0fj/88cf3312fa_random.cuda /tmp/tmpvoimt0fj/88cf3312fa_model.torch /tmp/tmpvoimt0fj/88cf3312fa_optim.torch /tmp/tmpvoimt0fj/88cf3312fa_optim.pyro /tmp/tmpvoimt0fj/88cf3312fa_params.pyro /tmp/tmpvoimt0fj/88cf3312fa_train.loaderstate /tmp/tmpvoimt0fj/88cf3312fa_test.loaderstate /tmp/tmpvoimt0fj/88cf3312fa_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/1511-Bipolar-dACC/1511-Bipolar-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Succeeded in writing posterior to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1511-Bipolar-dACC/1511-Bipolar-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:27:18 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1511-Bipolar-dACC/1511-Bipolar-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1511-Bipolar-dACC/1511-Bipolar-dACC.cellbender.output_cell_barcodes.csv cellbender:remove-background: Computing target noise counts per gene for MCKP estimator cellbender:remove-background: Using MCKP noise targets computed for FPR 0.01 cellbender:remove-background: Computing denoised counts using mckp estimator cellbender:remove-background: Working on chunk (1/7) cellbender:remove-background: [0.75 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 15:32:51 Total MCKP estimation time = 318.64 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/1511-Bipolar-dACC/1511-Bipolar-dACC.cellbender.output.h5 cellbender:remove-background: Succeeded in writing CellRanger format output to file /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1511-Bipolar-dACC/1511-Bipolar-dACC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1511-Bipolar-dACC/1511-Bipolar-dACC.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/1511-Bipolar-dACC/1511-Bipolar-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:33:08