cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1303-Schizophrenia-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1303-Schizophrenia-dACC/1303-Schizophrenia-dACC.cellbender.output.h5 --cuda --expected-cells 7468 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 3b908f7f75) cellbender:remove-background: 2024-06-06 15:11:03 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/1303-Schizophrenia-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: 31990 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 2795 cellbender:remove-background: Prior on counts for empty droplets is 122 cellbender:remove-background: Excluding 6823 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 25167 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 61 cellbender:remove-background: Using 7468 probable cell barcodes, plus an additional 12532 barcodes, and 23664 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 120 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmppzv6km86 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: 5737.2466 cellbender:remove-background: [epoch 002] average training loss: 4479.3628 (7.2 seconds per epoch) cellbender:remove-background: Will checkpoint every 59 epochs cellbender:remove-background: [epoch 003] average training loss: 3787.3085 cellbender:remove-background: [epoch 004] average training loss: 3359.0061 cellbender:remove-background: [epoch 005] average training loss: 3232.9986 cellbender:remove-background: [epoch 005] average test loss: 3427.0956 cellbender:remove-background: [epoch 006] average training loss: 3180.0623 cellbender:remove-background: [epoch 007] average training loss: 3135.4603 cellbender:remove-background: [epoch 008] average training loss: 3093.5506 cellbender:remove-background: [epoch 009] average training loss: 3053.9137 cellbender:remove-background: [epoch 010] average training loss: 2931.0960 cellbender:remove-background: [epoch 010] average test loss: 2937.6587 cellbender:remove-background: [epoch 011] average training loss: 2907.4518 cellbender:remove-background: [epoch 012] average training loss: 2885.2362 cellbender:remove-background: [epoch 013] average training loss: 2857.4031 cellbender:remove-background: [epoch 014] average training loss: 2869.8919 cellbender:remove-background: [epoch 015] average training loss: 2835.6073 cellbender:remove-background: [epoch 015] average test loss: 2909.0029 cellbender:remove-background: [epoch 016] average training loss: 2827.0740 cellbender:remove-background: [epoch 017] average training loss: 2836.0468 cellbender:remove-background: [epoch 018] average training loss: 2824.3492 cellbender:remove-background: [epoch 019] average training loss: 2814.4208 cellbender:remove-background: [epoch 020] average training loss: 2797.5086 cellbender:remove-background: [epoch 020] average test loss: 2846.2949 cellbender:remove-background: [epoch 021] average training loss: 2800.8900 cellbender:remove-background: [epoch 022] average training loss: 2798.1245 cellbender:remove-background: [epoch 023] average training loss: 2797.5926 cellbender:remove-background: [epoch 024] average training loss: 2790.1334 cellbender:remove-background: [epoch 025] average training loss: 2790.3632 cellbender:remove-background: [epoch 025] average test loss: 2811.9398 cellbender:remove-background: [epoch 026] average training loss: 2775.2411 cellbender:remove-background: [epoch 027] average training loss: 2774.6762 cellbender:remove-background: [epoch 028] average training loss: 2767.6945 cellbender:remove-background: [epoch 029] average training loss: 2753.8090 cellbender:remove-background: [epoch 030] average training loss: 2742.4373 cellbender:remove-background: [epoch 030] average test loss: 2762.1939 cellbender:remove-background: [epoch 031] average training loss: 2732.6617 cellbender:remove-background: [epoch 032] average training loss: 2728.2789 cellbender:remove-background: [epoch 033] average training loss: 2725.9425 cellbender:remove-background: [epoch 034] average training loss: 2725.9766 cellbender:remove-background: [epoch 035] average training loss: 2724.3315 cellbender:remove-background: [epoch 035] average test loss: 2750.0046 cellbender:remove-background: [epoch 036] average training loss: 2727.0962 cellbender:remove-background: [epoch 037] average training loss: 2726.3627 cellbender:remove-background: [epoch 038] average training loss: 2724.0300 cellbender:remove-background: [epoch 039] average training loss: 2723.8830 cellbender:remove-background: [epoch 040] average training loss: 2727.1185 cellbender:remove-background: [epoch 040] average test loss: 2766.0329 cellbender:remove-background: [epoch 041] average training loss: 2731.2941 cellbender:remove-background: [epoch 042] average training loss: 2731.2202 cellbender:remove-background: [epoch 043] average training loss: 2730.1434 cellbender:remove-background: [epoch 044] average training loss: 2729.2368 cellbender:remove-background: [epoch 045] average training loss: 2728.9397 cellbender:remove-background: [epoch 045] average test loss: 2765.3637 cellbender:remove-background: [epoch 046] average training loss: 2728.6560 cellbender:remove-background: [epoch 047] average training loss: 2730.4641 cellbender:remove-background: [epoch 048] average training loss: 2730.7148 cellbender:remove-background: [epoch 049] average training loss: 2734.6256 cellbender:remove-background: [epoch 050] average training loss: 2730.8207 cellbender:remove-background: [epoch 050] average test loss: 2784.3080 cellbender:remove-background: [epoch 051] average training loss: 2728.7981 cellbender:remove-background: [epoch 052] average training loss: 2731.7933 cellbender:remove-background: [epoch 053] average training loss: 2726.9537 cellbender:remove-background: [epoch 054] average training loss: 2722.1071 cellbender:remove-background: [epoch 055] average training loss: 2725.8406 cellbender:remove-background: [epoch 055] average test loss: 2764.2566 cellbender:remove-background: [epoch 056] average training loss: 2724.6943 cellbender:remove-background: [epoch 057] average training loss: 2724.4004 cellbender:remove-background: [epoch 058] average training loss: 2723.1098 cellbender:remove-background: [epoch 059] average training loss: 2723.9768 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/1303-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 060] average training loss: 2719.7026 cellbender:remove-background: [epoch 060] average test loss: 2757.1481 cellbender:remove-background: [epoch 061] average training loss: 2719.9721 cellbender:remove-background: [epoch 062] average training loss: 2722.0662 cellbender:remove-background: [epoch 063] average training loss: 2717.5402 cellbender:remove-background: [epoch 064] average training loss: 2723.5980 cellbender:remove-background: [epoch 065] average training loss: 2721.6757 cellbender:remove-background: [epoch 065] average test loss: 2761.3325 cellbender:remove-background: [epoch 066] average training loss: 2721.3142 cellbender:remove-background: [epoch 067] average training loss: 2724.7089 cellbender:remove-background: [epoch 068] average training loss: 2718.7005 cellbender:remove-background: [epoch 069] average training loss: 2718.4961 cellbender:remove-background: [epoch 070] average training loss: 2717.0389 cellbender:remove-background: [epoch 070] average test loss: 2772.1334 cellbender:remove-background: [epoch 071] average training loss: 2717.0741 cellbender:remove-background: [epoch 072] average training loss: 2718.3729 cellbender:remove-background: [epoch 073] average training loss: 2720.0611 cellbender:remove-background: [epoch 074] average training loss: 2721.5859 cellbender:remove-background: [epoch 075] average training loss: 2719.2213 cellbender:remove-background: [epoch 075] average test loss: 2764.9638 cellbender:remove-background: [epoch 076] average training loss: 2716.1874 cellbender:remove-background: [epoch 077] average training loss: 2719.7323 cellbender:remove-background: [epoch 078] average training loss: 2722.8452 cellbender:remove-background: [epoch 079] average training loss: 2717.8913 cellbender:remove-background: [epoch 080] average training loss: 2715.4206 cellbender:remove-background: [epoch 080] average test loss: 2769.9782 cellbender:remove-background: [epoch 081] average training loss: 2720.1698 cellbender:remove-background: [epoch 082] average training loss: 2711.2786 cellbender:remove-background: [epoch 083] average training loss: 2716.7450 cellbender:remove-background: [epoch 084] average training loss: 2713.2757 cellbender:remove-background: [epoch 085] average training loss: 2716.1965 cellbender:remove-background: [epoch 085] average test loss: 2776.2247 cellbender:remove-background: [epoch 086] average training loss: 2717.3466 cellbender:remove-background: [epoch 087] average training loss: 2715.3457 cellbender:remove-background: [epoch 088] average training loss: 2718.2344 cellbender:remove-background: [epoch 089] average training loss: 2717.3559 cellbender:remove-background: [epoch 090] average training loss: 2718.1893 cellbender:remove-background: [epoch 090] average test loss: 2796.0185 cellbender:remove-background: [epoch 091] average training loss: 2720.1575 cellbender:remove-background: [epoch 092] average training loss: 2718.3702 cellbender:remove-background: [epoch 093] average training loss: 2718.4825 cellbender:remove-background: [epoch 094] average training loss: 2717.8572 cellbender:remove-background: [epoch 095] average training loss: 2716.7863 cellbender:remove-background: [epoch 095] average test loss: 2778.8564 cellbender:remove-background: [epoch 096] average training loss: 2718.4122 cellbender:remove-background: [epoch 097] average training loss: 2719.1786 cellbender:remove-background: [epoch 098] average training loss: 2716.4058 cellbender:remove-background: [epoch 099] average training loss: 2719.5857 cellbender:remove-background: [epoch 100] average training loss: 2722.7580 cellbender:remove-background: [epoch 100] average test loss: 2774.5097 cellbender:remove-background: [epoch 101] average training loss: 2716.4054 cellbender:remove-background: [epoch 102] average training loss: 2718.0354 cellbender:remove-background: [epoch 103] average training loss: 2722.8626 cellbender:remove-background: [epoch 104] average training loss: 2711.7266 cellbender:remove-background: [epoch 105] average training loss: 2719.5995 cellbender:remove-background: [epoch 105] average test loss: 2780.2203 cellbender:remove-background: [epoch 106] average training loss: 2711.9667 cellbender:remove-background: [epoch 107] average training loss: 2714.6483 cellbender:remove-background: [epoch 108] average training loss: 2713.8106 cellbender:remove-background: [epoch 109] average training loss: 2713.0638 cellbender:remove-background: [epoch 110] average training loss: 2712.8424 cellbender:remove-background: [epoch 110] average test loss: 2789.3974 cellbender:remove-background: [epoch 111] average training loss: 2714.5006 cellbender:remove-background: [epoch 112] average training loss: 2714.4035 cellbender:remove-background: [epoch 113] average training loss: 2709.0689 cellbender:remove-background: [epoch 114] average training loss: 2712.7203 cellbender:remove-background: [epoch 115] average training loss: 2711.9463 cellbender:remove-background: [epoch 115] average test loss: 2783.8448 cellbender:remove-background: [epoch 116] average training loss: 2710.4502 cellbender:remove-background: [epoch 117] average training loss: 2712.6919 cellbender:remove-background: [epoch 118] average training loss: 2710.7574 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/1303-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 119] average training loss: 2705.1532 cellbender:remove-background: [epoch 120] average training loss: 2706.3689 cellbender:remove-background: [epoch 120] average test loss: 2776.1679 cellbender:remove-background: [epoch 121] average training loss: 2708.9459 cellbender:remove-background: [epoch 122] average training loss: 2707.1932 cellbender:remove-background: [epoch 123] average training loss: 2706.9327 cellbender:remove-background: [epoch 124] average training loss: 2707.3572 cellbender:remove-background: [epoch 125] average training loss: 2706.3954 cellbender:remove-background: [epoch 125] average test loss: 2768.6661 cellbender:remove-background: [epoch 126] average training loss: 2705.0873 cellbender:remove-background: [epoch 127] average training loss: 2706.0183 cellbender:remove-background: [epoch 128] average training loss: 2704.9166 cellbender:remove-background: [epoch 129] average training loss: 2707.3528 cellbender:remove-background: [epoch 130] average training loss: 2706.1492 cellbender:remove-background: [epoch 130] average test loss: 2789.3497 cellbender:remove-background: [epoch 131] average training loss: 2706.5013 cellbender:remove-background: [epoch 132] average training loss: 2704.2488 cellbender:remove-background: [epoch 133] average training loss: 2702.0687 cellbender:remove-background: [epoch 134] average training loss: 2701.5615 cellbender:remove-background: [epoch 135] average training loss: 2703.0271 cellbender:remove-background: [epoch 135] average test loss: 2784.9470 cellbender:remove-background: [epoch 136] average training loss: 2701.4648 cellbender:remove-background: [epoch 137] average training loss: 2704.4745 cellbender:remove-background: [epoch 138] average training loss: 2704.2338 cellbender:remove-background: [epoch 139] average training loss: 2702.9248 cellbender:remove-background: [epoch 140] average training loss: 2701.1483 cellbender:remove-background: [epoch 140] average test loss: 2775.1190 cellbender:remove-background: [epoch 141] average training loss: 2702.4979 cellbender:remove-background: [epoch 142] average training loss: 2702.8525 cellbender:remove-background: [epoch 143] average training loss: 2703.2165 cellbender:remove-background: [epoch 144] average training loss: 2702.8117 cellbender:remove-background: [epoch 145] average training loss: 2700.4941 cellbender:remove-background: [epoch 145] average test loss: 2768.0059 cellbender:remove-background: [epoch 146] average training loss: 2700.6613 cellbender:remove-background: [epoch 147] average training loss: 2701.9406 cellbender:remove-background: [epoch 148] average training loss: 2704.7170 cellbender:remove-background: [epoch 149] average training loss: 2703.1623 cellbender:remove-background: [epoch 150] average training loss: 2704.8543 cellbender:remove-background: [epoch 150] average test loss: 2769.3838 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/1303-Schizophrenia-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:32:16 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp9onoe87k cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp9onoe87k /tmp/tmp9onoe87k/3b908f7f75_random.pyro /tmp/tmp9onoe87k/3b908f7f75_random.cuda /tmp/tmp9onoe87k/3b908f7f75_model.torch /tmp/tmp9onoe87k/3b908f7f75_optim.torch /tmp/tmp9onoe87k/3b908f7f75_optim.pyro /tmp/tmp9onoe87k/3b908f7f75_params.pyro /tmp/tmp9onoe87k/3b908f7f75_train.loaderstate /tmp/tmp9onoe87k/3b908f7f75_test.loaderstate /tmp/tmp9onoe87k/3b908f7f75_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 (1/73) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/73) cellbender:remove-background: Working on chunk (3/73) cellbender:remove-background: Working on chunk (4/73) cellbender:remove-background: Working on chunk (5/73) cellbender:remove-background: Working on chunk (6/73) cellbender:remove-background: Working on chunk (7/73) cellbender:remove-background: Working on chunk (8/73) cellbender:remove-background: Working on chunk (9/73) cellbender:remove-background: Working on chunk (10/73) cellbender:remove-background: Working on chunk (11/73) cellbender:remove-background: Working on chunk (12/73) cellbender:remove-background: Working on chunk (13/73) cellbender:remove-background: Working on chunk (14/73) cellbender:remove-background: Working on chunk (15/73) cellbender:remove-background: Working on chunk (16/73) cellbender:remove-background: Working on chunk (17/73) cellbender:remove-background: Working on chunk (18/73) cellbender:remove-background: Working on chunk (19/73) cellbender:remove-background: Working on chunk (20/73) cellbender:remove-background: Working on chunk (21/73) cellbender:remove-background: Working on chunk (22/73) cellbender:remove-background: Working on chunk (23/73) cellbender:remove-background: Working on chunk (24/73) cellbender:remove-background: Working on chunk (25/73) cellbender:remove-background: Working on chunk (26/73) cellbender:remove-background: Working on chunk (27/73) cellbender:remove-background: Working on chunk (28/73) cellbender:remove-background: Working on chunk (29/73) cellbender:remove-background: Working on chunk (30/73) cellbender:remove-background: Working on chunk (31/73) cellbender:remove-background: Working on chunk (32/73) cellbender:remove-background: Working on chunk (33/73) cellbender:remove-background: Working on chunk (34/73) cellbender:remove-background: Working on chunk (35/73) cellbender:remove-background: Working on chunk (36/73) cellbender:remove-background: Working on chunk (37/73) cellbender:remove-background: Working on chunk (38/73) cellbender:remove-background: Working on chunk (39/73) cellbender:remove-background: Working on chunk (40/73) cellbender:remove-background: Working on chunk (41/73) cellbender:remove-background: Working on chunk (42/73) cellbender:remove-background: Working on chunk (43/73) cellbender:remove-background: Working on chunk (44/73) cellbender:remove-background: Working on chunk (45/73) cellbender:remove-background: Working on chunk (46/73) cellbender:remove-background: Working on chunk (47/73) cellbender:remove-background: Working on chunk (48/73) cellbender:remove-background: Working on chunk (49/73) cellbender:remove-background: Working on chunk (50/73) cellbender:remove-background: Working on chunk (51/73) cellbender:remove-background: Working on chunk (52/73) cellbender:remove-background: Working on chunk (53/73) cellbender:remove-background: Working on chunk (54/73) cellbender:remove-background: Working on chunk (55/73) cellbender:remove-background: Working on chunk (56/73) cellbender:remove-background: Working on chunk (57/73) cellbender:remove-background: Working on chunk (58/73) cellbender:remove-background: Working on chunk (59/73) cellbender:remove-background: Working on chunk (60/73) cellbender:remove-background: Working on chunk (61/73) cellbender:remove-background: Working on chunk (62/73) cellbender:remove-background: Working on chunk (63/73) cellbender:remove-background: Working on chunk (64/73) cellbender:remove-background: Working on chunk (65/73) cellbender:remove-background: Working on chunk (66/73) cellbender:remove-background: Working on chunk (67/73) cellbender:remove-background: Working on chunk (68/73) cellbender:remove-background: Working on chunk (69/73) cellbender:remove-background: Working on chunk (70/73) cellbender:remove-background: Working on chunk (71/73) cellbender:remove-background: Working on chunk (72/73) cellbender:remove-background: Working on chunk (73/73) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1303-Schizophrenia-dACC/1303-Schizophrenia-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/1303-Schizophrenia-dACC/1303-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:36:43 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1303-Schizophrenia-dACC/1303-Schizophrenia-dACC.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1303-Schizophrenia-dACC/1303-Schizophrenia-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: [1.22 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 15:45:40 Total MCKP estimation time = 514.18 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/1303-Schizophrenia-dACC/1303-Schizophrenia-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/1303-Schizophrenia-dACC/1303-Schizophrenia-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/1303-Schizophrenia-dACC/1303-Schizophrenia-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/1303-Schizophrenia-dACC/1303-Schizophrenia-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:45:56