cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2797-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-DLPFC/2797-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 6109 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 5f5e63b52d) cellbender:remove-background: 2024-06-06 15:11:38 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/2797-Schizophrenia-DLPFC.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: 31885 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 3182 cellbender:remove-background: Prior on counts for empty droplets is 105 cellbender:remove-background: Excluding 10264 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21621 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 52 cellbender:remove-background: Using 6109 probable cell barcodes, plus an additional 13891 barcodes, and 30588 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 104 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpcyjcwswh 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: 4942.8645 cellbender:remove-background: [epoch 002] average training loss: 3897.6309 (6.5 seconds per epoch) cellbender:remove-background: Will checkpoint every 65 epochs cellbender:remove-background: [epoch 003] average training loss: 3336.0308 cellbender:remove-background: [epoch 004] average training loss: 3007.3492 cellbender:remove-background: [epoch 005] average training loss: 2912.6215 cellbender:remove-background: [epoch 005] average test loss: 3028.2923 cellbender:remove-background: [epoch 006] average training loss: 2871.9457 cellbender:remove-background: [epoch 007] average training loss: 2835.1980 cellbender:remove-background: [epoch 008] average training loss: 2805.9994 cellbender:remove-background: [epoch 009] average training loss: 2784.7863 cellbender:remove-background: [epoch 010] average training loss: 2729.4228 cellbender:remove-background: [epoch 010] average test loss: 2743.9280 cellbender:remove-background: [epoch 011] average training loss: 2697.6492 cellbender:remove-background: [epoch 012] average training loss: 2679.0663 cellbender:remove-background: [epoch 013] average training loss: 2662.5061 cellbender:remove-background: [epoch 014] average training loss: 2669.7573 cellbender:remove-background: [epoch 015] average training loss: 2647.1216 cellbender:remove-background: [epoch 015] average test loss: 2665.4909 cellbender:remove-background: [epoch 016] average training loss: 2644.5135 cellbender:remove-background: [epoch 017] average training loss: 2651.2848 cellbender:remove-background: [epoch 018] average training loss: 2644.1393 cellbender:remove-background: [epoch 019] average training loss: 2634.2253 cellbender:remove-background: [epoch 020] average training loss: 2618.5894 cellbender:remove-background: [epoch 020] average test loss: 2650.3404 cellbender:remove-background: [epoch 021] average training loss: 2618.9490 cellbender:remove-background: [epoch 022] average training loss: 2617.2447 cellbender:remove-background: [epoch 023] average training loss: 2610.6657 cellbender:remove-background: [epoch 024] average training loss: 2603.6525 cellbender:remove-background: [epoch 025] average training loss: 2599.3739 cellbender:remove-background: [epoch 025] average test loss: 2602.1743 cellbender:remove-background: [epoch 026] average training loss: 2581.9452 cellbender:remove-background: [epoch 027] average training loss: 2560.1775 cellbender:remove-background: [epoch 028] average training loss: 2546.6282 cellbender:remove-background: [epoch 029] average training loss: 2539.0839 cellbender:remove-background: [epoch 030] average training loss: 2531.6942 cellbender:remove-background: [epoch 030] average test loss: 2523.7522 cellbender:remove-background: [epoch 031] average training loss: 2526.9250 cellbender:remove-background: [epoch 032] average training loss: 2522.6594 cellbender:remove-background: [epoch 033] average training loss: 2521.4888 cellbender:remove-background: [epoch 034] average training loss: 2517.7582 cellbender:remove-background: [epoch 035] average training loss: 2518.3968 cellbender:remove-background: [epoch 035] average test loss: 2496.6092 cellbender:remove-background: [epoch 036] average training loss: 2516.1990 cellbender:remove-background: [epoch 037] average training loss: 2515.7632 cellbender:remove-background: [epoch 038] average training loss: 2513.7597 cellbender:remove-background: [epoch 039] average training loss: 2510.8323 cellbender:remove-background: [epoch 040] average training loss: 2510.6382 cellbender:remove-background: [epoch 040] average test loss: 2498.2579 cellbender:remove-background: [epoch 041] average training loss: 2511.2128 cellbender:remove-background: [epoch 042] average training loss: 2509.3016 cellbender:remove-background: [epoch 043] average training loss: 2509.6594 cellbender:remove-background: [epoch 044] average training loss: 2503.6635 cellbender:remove-background: [epoch 045] average training loss: 2505.4074 cellbender:remove-background: [epoch 045] average test loss: 2487.0566 cellbender:remove-background: [epoch 046] average training loss: 2507.3804 cellbender:remove-background: [epoch 047] average training loss: 2504.6470 cellbender:remove-background: [epoch 048] average training loss: 2504.1398 cellbender:remove-background: [epoch 049] average training loss: 2503.1449 cellbender:remove-background: [epoch 050] average training loss: 2506.3521 cellbender:remove-background: [epoch 050] average test loss: 2492.8625 cellbender:remove-background: [epoch 051] average training loss: 2504.8153 cellbender:remove-background: [epoch 052] average training loss: 2505.5747 cellbender:remove-background: [epoch 053] average training loss: 2506.8771 cellbender:remove-background: [epoch 054] average training loss: 2507.5158 cellbender:remove-background: [epoch 055] average training loss: 2510.3191 cellbender:remove-background: [epoch 055] average test loss: 2544.2089 cellbender:remove-background: [epoch 056] average training loss: 2509.7910 cellbender:remove-background: [epoch 057] average training loss: 2508.4886 cellbender:remove-background: [epoch 058] average training loss: 2508.2012 cellbender:remove-background: [epoch 059] average training loss: 2510.6666 cellbender:remove-background: [epoch 060] average training loss: 2512.7276 cellbender:remove-background: [epoch 060] average test loss: 2504.3427 cellbender:remove-background: [epoch 061] average training loss: 2507.1644 cellbender:remove-background: [epoch 062] average training loss: 2519.7197 cellbender:remove-background: [epoch 063] average training loss: 2509.6924 cellbender:remove-background: [epoch 064] average training loss: 2517.6823 cellbender:remove-background: [epoch 065] average training loss: 2523.8684 cellbender:remove-background: [epoch 065] average test loss: 2515.4131 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/2797-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 066] average training loss: 2519.2337 cellbender:remove-background: [epoch 067] average training loss: 2531.5704 cellbender:remove-background: [epoch 068] average training loss: 2539.2848 cellbender:remove-background: [epoch 069] average training loss: 2540.2517 cellbender:remove-background: [epoch 070] average training loss: 2535.8173 cellbender:remove-background: [epoch 070] average test loss: 2535.0452 cellbender:remove-background: [epoch 071] average training loss: 2538.1871 cellbender:remove-background: [epoch 072] average training loss: 2543.0161 cellbender:remove-background: [epoch 073] average training loss: 2542.8145 cellbender:remove-background: [epoch 074] average training loss: 2539.1240 cellbender:remove-background: [epoch 075] average training loss: 2545.1938 cellbender:remove-background: [epoch 075] average test loss: 2536.3433 cellbender:remove-background: [epoch 076] average training loss: 2537.1112 cellbender:remove-background: [epoch 077] average training loss: 2546.3631 cellbender:remove-background: [epoch 078] average training loss: 2541.9178 cellbender:remove-background: [epoch 079] average training loss: 2545.3856 cellbender:remove-background: [epoch 080] average training loss: 2549.3307 cellbender:remove-background: [epoch 080] average test loss: 2610.1849 cellbender:remove-background: [epoch 081] average training loss: 2557.5111 cellbender:remove-background: [epoch 082] average training loss: 2558.2608 cellbender:remove-background: [epoch 083] average training loss: 2566.1421 cellbender:remove-background: [epoch 084] average training loss: 2550.9092 cellbender:remove-background: [epoch 085] average training loss: 2545.9021 cellbender:remove-background: [epoch 085] average test loss: 2571.0107 cellbender:remove-background: [epoch 086] average training loss: 2561.3810 cellbender:remove-background: [epoch 087] average training loss: 2577.6178 cellbender:remove-background: [epoch 088] average training loss: 2544.0750 cellbender:remove-background: [epoch 089] average training loss: 2556.3809 cellbender:remove-background: [epoch 090] average training loss: 2541.7397 cellbender:remove-background: [epoch 090] average test loss: 2574.8000 cellbender:remove-background: [epoch 091] average training loss: 2549.6838 cellbender:remove-background: [epoch 092] average training loss: 2566.1191 cellbender:remove-background: [epoch 093] average training loss: 2555.1379 cellbender:remove-background: [epoch 094] average training loss: 2553.4999 cellbender:remove-background: [epoch 095] average training loss: 2548.6991 cellbender:remove-background: [epoch 095] average test loss: 2607.8471 cellbender:remove-background: [epoch 096] average training loss: 2553.0934 cellbender:remove-background: [epoch 097] average training loss: 2560.7928 cellbender:remove-background: [epoch 098] average training loss: 2556.6961 cellbender:remove-background: [epoch 099] average training loss: 2535.6595 cellbender:remove-background: [epoch 100] average training loss: 2558.0757 cellbender:remove-background: [epoch 100] average test loss: 2582.7959 cellbender:remove-background: [epoch 101] average training loss: 2552.5669 cellbender:remove-background: [epoch 102] average training loss: 2547.5768 cellbender:remove-background: [epoch 103] average training loss: 2545.8227 cellbender:remove-background: [epoch 104] average training loss: 2551.7289 cellbender:remove-background: [epoch 105] average training loss: 2552.3657 cellbender:remove-background: [epoch 105] average test loss: 2603.5543 cellbender:remove-background: [epoch 106] average training loss: 2544.4004 cellbender:remove-background: [epoch 107] average training loss: 2546.2882 cellbender:remove-background: [epoch 108] average training loss: 2535.8738 cellbender:remove-background: [epoch 109] average training loss: 2538.1299 cellbender:remove-background: [epoch 110] average training loss: 2532.1859 cellbender:remove-background: [epoch 110] average test loss: 2567.6524 cellbender:remove-background: [epoch 111] average training loss: 2537.1630 cellbender:remove-background: [epoch 112] average training loss: 2537.9039 cellbender:remove-background: [epoch 113] average training loss: 2543.3503 cellbender:remove-background: [epoch 114] average training loss: 2532.4020 cellbender:remove-background: [epoch 115] average training loss: 2552.4897 cellbender:remove-background: [epoch 115] average test loss: 2595.7582 cellbender:remove-background: [epoch 116] average training loss: 2544.7195 cellbender:remove-background: [epoch 117] average training loss: 2533.7798 cellbender:remove-background: [epoch 118] average training loss: 2546.9903 cellbender:remove-background: [epoch 119] average training loss: 2526.0746 cellbender:remove-background: [epoch 120] average training loss: 2545.0948 cellbender:remove-background: [epoch 120] average test loss: 2609.7170 cellbender:remove-background: [epoch 121] average training loss: 2537.8790 cellbender:remove-background: [epoch 122] average training loss: 2534.1134 cellbender:remove-background: [epoch 123] average training loss: 2539.3806 cellbender:remove-background: [epoch 124] average training loss: 2532.9927 cellbender:remove-background: [epoch 125] average training loss: 2530.4069 cellbender:remove-background: [epoch 125] average test loss: 2569.8346 cellbender:remove-background: [epoch 126] average training loss: 2546.3186 cellbender:remove-background: [epoch 127] average training loss: 2544.5746 cellbender:remove-background: [epoch 128] average training loss: 2523.9964 cellbender:remove-background: [epoch 129] average training loss: 2531.6907 cellbender:remove-background: [epoch 130] average training loss: 2541.0655 cellbender:remove-background: [epoch 130] average test loss: 2572.7141 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/2797-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 131] average training loss: 2551.4334 cellbender:remove-background: [epoch 132] average training loss: 2534.5291 cellbender:remove-background: [epoch 133] average training loss: 2543.3478 cellbender:remove-background: [epoch 134] average training loss: 2541.6158 cellbender:remove-background: [epoch 135] average training loss: 2536.8155 cellbender:remove-background: [epoch 135] average test loss: 2597.3865 cellbender:remove-background: [epoch 136] average training loss: 2532.5844 cellbender:remove-background: [epoch 137] average training loss: 2531.9233 cellbender:remove-background: [epoch 138] average training loss: 2535.1217 cellbender:remove-background: [epoch 139] average training loss: 2545.3882 cellbender:remove-background: [epoch 140] average training loss: 2529.7033 cellbender:remove-background: [epoch 140] average test loss: 2570.1598 cellbender:remove-background: [epoch 141] average training loss: 2537.1415 cellbender:remove-background: [epoch 142] average training loss: 2523.6543 cellbender:remove-background: [epoch 143] average training loss: 2537.5865 cellbender:remove-background: [epoch 144] average training loss: 2535.8967 cellbender:remove-background: [epoch 145] average training loss: 2531.7082 cellbender:remove-background: [epoch 145] average test loss: 2605.5083 cellbender:remove-background: [epoch 146] average training loss: 2534.0141 cellbender:remove-background: [epoch 147] average training loss: 2536.7517 cellbender:remove-background: [epoch 148] average training loss: 2529.9313 cellbender:remove-background: [epoch 149] average training loss: 2530.6722 cellbender:remove-background: [epoch 150] average training loss: 2534.4236 cellbender:remove-background: [epoch 150] average test loss: 2634.0247 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/2797-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:31:09 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp_5940kmy cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp_5940kmy /tmp/tmp_5940kmy/5f5e63b52d_random.pyro /tmp/tmp_5940kmy/5f5e63b52d_random.cuda /tmp/tmp_5940kmy/5f5e63b52d_model.torch /tmp/tmp_5940kmy/5f5e63b52d_optim.torch /tmp/tmp_5940kmy/5f5e63b52d_optim.pyro /tmp/tmp_5940kmy/5f5e63b52d_params.pyro /tmp/tmp_5940kmy/5f5e63b52d_train.loaderstate /tmp/tmp_5940kmy/5f5e63b52d_test.loaderstate /tmp/tmp_5940kmy/5f5e63b52d_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/2797-Schizophrenia-DLPFC/2797-Schizophrenia-DLPFC.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/2797-Schizophrenia-DLPFC/2797-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:35:20 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-DLPFC/2797-Schizophrenia-DLPFC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-DLPFC/2797-Schizophrenia-DLPFC.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: [1.60 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 15:47:02 Total MCKP estimation time = 676.04 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/2797-Schizophrenia-DLPFC/2797-Schizophrenia-DLPFC.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/2797-Schizophrenia-DLPFC/2797-Schizophrenia-DLPFC.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2797-Schizophrenia-DLPFC/2797-Schizophrenia-DLPFC.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/2797-Schizophrenia-DLPFC/2797-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:47:19