cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2780-Control-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-Hippocampus/2780-Control-Hippocampus.cellbender.output.h5 --cuda --expected-cells 6892 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash e86535e114) cellbender:remove-background: 2024-06-06 15:38:06 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/2780-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: 31774 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3020 cellbender:remove-background: Prior on counts for empty droplets is 46 cellbender:remove-background: Excluding 12146 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 19628 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 23 cellbender:remove-background: Using 6892 probable cell barcodes, plus an additional 13108 barcodes, and 41771 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 45 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp_0iwcmn7 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: 4691.4743 cellbender:remove-background: [epoch 002] average training loss: 3704.9815 (6.0 seconds per epoch) cellbender:remove-background: Will checkpoint every 71 epochs cellbender:remove-background: [epoch 003] average training loss: 3176.9019 cellbender:remove-background: [epoch 004] average training loss: 2904.9650 cellbender:remove-background: [epoch 005] average training loss: 2847.8011 cellbender:remove-background: [epoch 005] average test loss: 2909.2421 cellbender:remove-background: [epoch 006] average training loss: 2834.7417 cellbender:remove-background: [epoch 007] average training loss: 2801.6794 cellbender:remove-background: [epoch 008] average training loss: 2769.8803 cellbender:remove-background: [epoch 009] average training loss: 2766.4951 cellbender:remove-background: [epoch 010] average training loss: 2700.0510 cellbender:remove-background: [epoch 010] average test loss: 2823.2579 cellbender:remove-background: [epoch 011] average training loss: 2597.7343 cellbender:remove-background: [epoch 012] average training loss: 2548.9363 cellbender:remove-background: [epoch 013] average training loss: 2522.0124 cellbender:remove-background: [epoch 014] average training loss: 2535.5114 cellbender:remove-background: [epoch 015] average training loss: 2448.7538 cellbender:remove-background: [epoch 015] average test loss: 2444.8388 cellbender:remove-background: [epoch 016] average training loss: 2373.7992 cellbender:remove-background: [epoch 017] average training loss: 2366.1916 cellbender:remove-background: [epoch 018] average training loss: 2352.4444 cellbender:remove-background: [epoch 019] average training loss: 2338.4845 cellbender:remove-background: [epoch 020] average training loss: 2320.8332 cellbender:remove-background: [epoch 020] average test loss: 2336.3134 cellbender:remove-background: [epoch 021] average training loss: 2314.4980 cellbender:remove-background: [epoch 022] average training loss: 2300.5040 cellbender:remove-background: [epoch 023] average training loss: 2287.3314 cellbender:remove-background: [epoch 024] average training loss: 2271.7819 cellbender:remove-background: [epoch 025] average training loss: 2267.6492 cellbender:remove-background: [epoch 025] average test loss: 2276.9611 cellbender:remove-background: [epoch 026] average training loss: 2253.4882 cellbender:remove-background: [epoch 027] average training loss: 2250.9861 cellbender:remove-background: [epoch 028] average training loss: 2248.5253 cellbender:remove-background: [epoch 029] average training loss: 2240.6896 cellbender:remove-background: [epoch 030] average training loss: 2236.4298 cellbender:remove-background: [epoch 030] average test loss: 2233.9619 cellbender:remove-background: [epoch 031] average training loss: 2233.9642 cellbender:remove-background: [epoch 032] average training loss: 2228.8170 cellbender:remove-background: [epoch 033] average training loss: 2228.2620 cellbender:remove-background: [epoch 034] average training loss: 2225.2236 cellbender:remove-background: [epoch 035] average training loss: 2223.4453 cellbender:remove-background: [epoch 035] average test loss: 2216.3817 cellbender:remove-background: [epoch 036] average training loss: 2220.1213 cellbender:remove-background: [epoch 037] average training loss: 2218.4546 cellbender:remove-background: [epoch 038] average training loss: 2217.0612 cellbender:remove-background: [epoch 039] average training loss: 2214.6079 cellbender:remove-background: [epoch 040] average training loss: 2216.1767 cellbender:remove-background: [epoch 040] average test loss: 2223.8537 cellbender:remove-background: [epoch 041] average training loss: 2214.5908 cellbender:remove-background: [epoch 042] average training loss: 2215.7786 cellbender:remove-background: [epoch 043] average training loss: 2215.1158 cellbender:remove-background: [epoch 044] average training loss: 2213.8155 cellbender:remove-background: [epoch 045] average training loss: 2213.9318 cellbender:remove-background: [epoch 045] average test loss: 2206.1469 cellbender:remove-background: [epoch 046] average training loss: 2213.6821 cellbender:remove-background: [epoch 047] average training loss: 2211.8357 cellbender:remove-background: [epoch 048] average training loss: 2216.2702 cellbender:remove-background: [epoch 049] average training loss: 2218.9615 cellbender:remove-background: [epoch 050] average training loss: 2220.6245 cellbender:remove-background: [epoch 050] average test loss: 2233.8492 cellbender:remove-background: [epoch 051] average training loss: 2235.5583 cellbender:remove-background: [epoch 052] average training loss: 2237.1912 cellbender:remove-background: [epoch 053] average training loss: 2235.7522 cellbender:remove-background: [epoch 054] average training loss: 2245.9574 cellbender:remove-background: [epoch 055] average training loss: 2234.3445 cellbender:remove-background: [epoch 055] average test loss: 2271.3076 cellbender:remove-background: [epoch 056] average training loss: 2250.0334 cellbender:remove-background: [epoch 057] average training loss: 2239.6240 cellbender:remove-background: [epoch 058] average training loss: 2239.7939 cellbender:remove-background: [epoch 059] average training loss: 2239.6481 cellbender:remove-background: [epoch 060] average training loss: 2237.6121 cellbender:remove-background: [epoch 060] average test loss: 2220.9268 cellbender:remove-background: [epoch 061] average training loss: 2236.5056 cellbender:remove-background: [epoch 062] average training loss: 2243.1670 cellbender:remove-background: [epoch 063] average training loss: 2236.7488 cellbender:remove-background: [epoch 064] average training loss: 2246.7064 cellbender:remove-background: [epoch 065] average training loss: 2250.1977 cellbender:remove-background: [epoch 065] average test loss: 2280.3557 cellbender:remove-background: [epoch 066] average training loss: 2260.1800 cellbender:remove-background: [epoch 067] average training loss: 2241.5408 cellbender:remove-background: [epoch 068] average training loss: 2240.6018 cellbender:remove-background: [epoch 069] average training loss: 2247.9763 cellbender:remove-background: [epoch 070] average training loss: 2245.5952 cellbender:remove-background: [epoch 070] average test loss: 2270.4877 cellbender:remove-background: [epoch 071] average training loss: 2250.1097 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/2780-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 072] average training loss: 2241.7460 cellbender:remove-background: [epoch 073] average training loss: 2249.1704 cellbender:remove-background: [epoch 074] average training loss: 2254.0416 cellbender:remove-background: [epoch 075] average training loss: 2246.4369 cellbender:remove-background: [epoch 075] average test loss: 2273.7647 cellbender:remove-background: [epoch 076] average training loss: 2244.2217 cellbender:remove-background: [epoch 077] average training loss: 2245.8417 cellbender:remove-background: [epoch 078] average training loss: 2248.3725 cellbender:remove-background: [epoch 079] average training loss: 2244.1539 cellbender:remove-background: [epoch 080] average training loss: 2245.0747 cellbender:remove-background: [epoch 080] average test loss: 2281.6565 cellbender:remove-background: [epoch 081] average training loss: 2245.1186 cellbender:remove-background: [epoch 082] average training loss: 2245.7616 cellbender:remove-background: [epoch 083] average training loss: 2247.1466 cellbender:remove-background: [epoch 084] average training loss: 2245.5364 cellbender:remove-background: [epoch 085] average training loss: 2245.7967 cellbender:remove-background: [epoch 085] average test loss: 2266.2118 cellbender:remove-background: [epoch 086] average training loss: 2248.8181 cellbender:remove-background: [epoch 087] average training loss: 2247.6879 cellbender:remove-background: [epoch 088] average training loss: 2243.0466 cellbender:remove-background: [epoch 089] average training loss: 2243.2624 cellbender:remove-background: [epoch 090] average training loss: 2242.1455 cellbender:remove-background: [epoch 090] average test loss: 2271.1573 cellbender:remove-background: [epoch 091] average training loss: 2240.0842 cellbender:remove-background: [epoch 092] average training loss: 2242.7429 cellbender:remove-background: [epoch 093] average training loss: 2242.4004 cellbender:remove-background: [epoch 094] average training loss: 2245.4148 cellbender:remove-background: [epoch 095] average training loss: 2243.1203 cellbender:remove-background: [epoch 095] average test loss: 2274.3686 cellbender:remove-background: [epoch 096] average training loss: 2241.0997 cellbender:remove-background: [epoch 097] average training loss: 2242.8319 cellbender:remove-background: [epoch 098] average training loss: 2243.5994 cellbender:remove-background: [epoch 099] average training loss: 2241.4283 cellbender:remove-background: [epoch 100] average training loss: 2243.2461 cellbender:remove-background: [epoch 100] average test loss: 2275.6708 cellbender:remove-background: [epoch 101] average training loss: 2241.3954 cellbender:remove-background: [epoch 102] average training loss: 2241.4534 cellbender:remove-background: [epoch 103] average training loss: 2241.1840 cellbender:remove-background: [epoch 104] average training loss: 2239.6013 cellbender:remove-background: [epoch 105] average training loss: 2238.6494 cellbender:remove-background: [epoch 105] average test loss: 2263.1500 cellbender:remove-background: [epoch 106] average training loss: 2239.4530 cellbender:remove-background: [epoch 107] average training loss: 2239.4534 cellbender:remove-background: [epoch 108] average training loss: 2241.9132 cellbender:remove-background: [epoch 109] average training loss: 2238.3399 cellbender:remove-background: [epoch 110] average training loss: 2238.2622 cellbender:remove-background: [epoch 110] average test loss: 2274.5800 cellbender:remove-background: [epoch 111] average training loss: 2241.2983 cellbender:remove-background: [epoch 112] average training loss: 2234.5144 cellbender:remove-background: [epoch 113] average training loss: 2238.6632 cellbender:remove-background: [epoch 114] average training loss: 2238.7722 cellbender:remove-background: [epoch 115] average training loss: 2235.6221 cellbender:remove-background: [epoch 115] average test loss: 2277.9565 cellbender:remove-background: [epoch 116] average training loss: 2237.4521 cellbender:remove-background: [epoch 117] average training loss: 2234.8058 cellbender:remove-background: [epoch 118] average training loss: 2235.2845 cellbender:remove-background: [epoch 119] average training loss: 2234.0145 cellbender:remove-background: [epoch 120] average training loss: 2236.6692 cellbender:remove-background: [epoch 120] average test loss: 2256.9779 cellbender:remove-background: [epoch 121] average training loss: 2231.9279 cellbender:remove-background: [epoch 122] average training loss: 2233.6703 cellbender:remove-background: [epoch 123] average training loss: 2235.9178 cellbender:remove-background: [epoch 124] average training loss: 2233.9424 cellbender:remove-background: [epoch 125] average training loss: 2236.5366 cellbender:remove-background: [epoch 125] average test loss: 2278.6585 cellbender:remove-background: [epoch 126] average training loss: 2236.3168 cellbender:remove-background: [epoch 127] average training loss: 2234.6520 cellbender:remove-background: [epoch 128] average training loss: 2234.2848 cellbender:remove-background: [epoch 129] average training loss: 2231.0851 cellbender:remove-background: [epoch 130] average training loss: 2236.4777 cellbender:remove-background: [epoch 130] average test loss: 2266.6423 cellbender:remove-background: [epoch 131] average training loss: 2230.2081 cellbender:remove-background: [epoch 132] average training loss: 2233.6999 cellbender:remove-background: [epoch 133] average training loss: 2232.8574 cellbender:remove-background: [epoch 134] average training loss: 2233.5532 cellbender:remove-background: [epoch 135] average training loss: 2233.6493 cellbender:remove-background: [epoch 135] average test loss: 2276.6627 cellbender:remove-background: [epoch 136] average training loss: 2231.5392 cellbender:remove-background: [epoch 137] average training loss: 2228.8250 cellbender:remove-background: [epoch 138] average training loss: 2232.0462 cellbender:remove-background: [epoch 139] average training loss: 2231.2047 cellbender:remove-background: [epoch 140] average training loss: 2231.6229 cellbender:remove-background: [epoch 140] average test loss: 2270.3195 cellbender:remove-background: [epoch 141] average training loss: 2233.0635 cellbender:remove-background: [epoch 142] average training loss: 2232.0013 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/2780-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 143] average training loss: 2232.4432 cellbender:remove-background: [epoch 144] average training loss: 2231.2750 cellbender:remove-background: [epoch 145] average training loss: 2232.0547 cellbender:remove-background: [epoch 145] average test loss: 2269.0881 cellbender:remove-background: [epoch 146] average training loss: 2232.1288 cellbender:remove-background: [epoch 147] average training loss: 2231.6955 cellbender:remove-background: [epoch 148] average training loss: 2231.1709 cellbender:remove-background: [epoch 149] average training loss: 2231.4554 cellbender:remove-background: [epoch 150] average training loss: 2231.7571 cellbender:remove-background: [epoch 150] average test loss: 2268.7185 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/2780-Control-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:57:24 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpejqpc9k_ cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpejqpc9k_ /tmp/tmpejqpc9k_/e86535e114_random.pyro /tmp/tmpejqpc9k_/e86535e114_random.cuda /tmp/tmpejqpc9k_/e86535e114_model.torch /tmp/tmpejqpc9k_/e86535e114_optim.torch /tmp/tmpejqpc9k_/e86535e114_optim.pyro /tmp/tmpejqpc9k_/e86535e114_params.pyro /tmp/tmpejqpc9k_/e86535e114_train.loaderstate /tmp/tmpejqpc9k_/e86535e114_test.loaderstate /tmp/tmpejqpc9k_/e86535e114_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 (1/62) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/62) cellbender:remove-background: Working on chunk (3/62) cellbender:remove-background: Working on chunk (4/62) cellbender:remove-background: Working on chunk (5/62) cellbender:remove-background: Working on chunk (6/62) cellbender:remove-background: Working on chunk (7/62) cellbender:remove-background: Working on chunk (8/62) cellbender:remove-background: Working on chunk (9/62) cellbender:remove-background: Working on chunk (10/62) cellbender:remove-background: Working on chunk (11/62) cellbender:remove-background: Working on chunk (12/62) cellbender:remove-background: Working on chunk (13/62) cellbender:remove-background: Working on chunk (14/62) cellbender:remove-background: Working on chunk (15/62) cellbender:remove-background: Working on chunk (16/62) cellbender:remove-background: Working on chunk (17/62) cellbender:remove-background: Working on chunk (18/62) cellbender:remove-background: Working on chunk (19/62) cellbender:remove-background: Working on chunk (20/62) cellbender:remove-background: Working on chunk (21/62) cellbender:remove-background: Working on chunk (22/62) cellbender:remove-background: Working on chunk (23/62) cellbender:remove-background: Working on chunk (24/62) cellbender:remove-background: Working on chunk (25/62) cellbender:remove-background: Working on chunk (26/62) cellbender:remove-background: Working on chunk (27/62) cellbender:remove-background: Working on chunk (28/62) cellbender:remove-background: Working on chunk (29/62) cellbender:remove-background: Working on chunk (30/62) cellbender:remove-background: Working on chunk (31/62) cellbender:remove-background: Working on chunk (32/62) cellbender:remove-background: Working on chunk (33/62) cellbender:remove-background: Working on chunk (34/62) cellbender:remove-background: Working on chunk (35/62) cellbender:remove-background: Working on chunk (36/62) cellbender:remove-background: Working on chunk (37/62) cellbender:remove-background: Working on chunk (38/62) cellbender:remove-background: Working on chunk (39/62) cellbender:remove-background: Working on chunk (40/62) cellbender:remove-background: Working on chunk (41/62) cellbender:remove-background: Working on chunk (42/62) cellbender:remove-background: Working on chunk (43/62) cellbender:remove-background: Working on chunk (44/62) cellbender:remove-background: Working on chunk (45/62) cellbender:remove-background: Working on chunk (46/62) cellbender:remove-background: Working on chunk (47/62) cellbender:remove-background: Working on chunk (48/62) cellbender:remove-background: Working on chunk (49/62) cellbender:remove-background: Working on chunk (50/62) cellbender:remove-background: Working on chunk (51/62) cellbender:remove-background: Working on chunk (52/62) cellbender:remove-background: Working on chunk (53/62) cellbender:remove-background: Working on chunk (54/62) cellbender:remove-background: Working on chunk (55/62) cellbender:remove-background: Working on chunk (56/62) cellbender:remove-background: Working on chunk (57/62) cellbender:remove-background: Working on chunk (58/62) cellbender:remove-background: Working on chunk (59/62) cellbender:remove-background: Working on chunk (60/62) cellbender:remove-background: Working on chunk (61/62) cellbender:remove-background: Working on chunk (62/62) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-Hippocampus/2780-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/2780-Control-Hippocampus/2780-Control-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:01:15 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2780-Control-Hippocampus/2780-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/2780-Control-Hippocampus/2780-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: [1.45 mins per chunk] cellbender:remove-background: Working on chunk (2/7) cellbender:remove-background: Working on chunk (3/7) cellbender:remove-background: Working on chunk (4/7) cellbender:remove-background: Working on chunk (5/7) cellbender:remove-background: Working on chunk (6/7) cellbender:remove-background: Working on chunk (7/7) cellbender:remove-background: 2024-06-06 16:11:47 Total MCKP estimation time = 606.91 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/2780-Control-Hippocampus/2780-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/2780-Control-Hippocampus/2780-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/2780-Control-Hippocampus/2780-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/2780-Control-Hippocampus/2780-Control-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:12:04