cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1676-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1676-Schizophrenia-DLPFC/1676-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 7034 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 3e2e5bdedb) cellbender:remove-background: 2024-06-06 15:36:59 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/1676-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: 31929 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 5701 cellbender:remove-background: Prior on counts for empty droplets is 30 cellbender:remove-background: Excluding 13818 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 18111 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 15 cellbender:remove-background: Using 7034 probable cell barcodes, plus an additional 12966 barcodes, and 42174 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 29 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpvjaynlsn 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: 6431.6834 cellbender:remove-background: [epoch 002] average training loss: 4999.0867 (5.3 seconds per epoch) cellbender:remove-background: Will checkpoint every 80 epochs cellbender:remove-background: [epoch 003] average training loss: 4243.7610 cellbender:remove-background: [epoch 004] average training loss: 3754.6380 cellbender:remove-background: [epoch 005] average training loss: 3543.4747 cellbender:remove-background: [epoch 005] average test loss: 3478.2854 cellbender:remove-background: [epoch 006] average training loss: 3408.0880 cellbender:remove-background: [epoch 007] average training loss: 3305.0168 cellbender:remove-background: [epoch 008] average training loss: 3261.5000 cellbender:remove-background: [epoch 009] average training loss: 3250.9124 cellbender:remove-background: [epoch 010] average training loss: 3209.5027 cellbender:remove-background: [epoch 010] average test loss: 3179.0796 cellbender:remove-background: [epoch 011] average training loss: 3149.7111 cellbender:remove-background: [epoch 012] average training loss: 2980.4740 cellbender:remove-background: [epoch 013] average training loss: 2934.4135 cellbender:remove-background: [epoch 014] average training loss: 2930.7108 cellbender:remove-background: [epoch 015] average training loss: 2888.9016 cellbender:remove-background: [epoch 015] average test loss: 2877.8865 cellbender:remove-background: [epoch 016] average training loss: 2864.5673 cellbender:remove-background: [epoch 017] average training loss: 2858.6566 cellbender:remove-background: [epoch 018] average training loss: 2841.3492 cellbender:remove-background: [epoch 019] average training loss: 2824.3558 cellbender:remove-background: [epoch 020] average training loss: 2799.3210 cellbender:remove-background: [epoch 020] average test loss: 2780.8199 cellbender:remove-background: [epoch 021] average training loss: 2784.6243 cellbender:remove-background: [epoch 022] average training loss: 2774.2314 cellbender:remove-background: [epoch 023] average training loss: 2768.4530 cellbender:remove-background: [epoch 024] average training loss: 2755.9540 cellbender:remove-background: [epoch 025] average training loss: 2753.7314 cellbender:remove-background: [epoch 025] average test loss: 2721.8836 cellbender:remove-background: [epoch 026] average training loss: 2743.9333 cellbender:remove-background: [epoch 027] average training loss: 2739.9189 cellbender:remove-background: [epoch 028] average training loss: 2737.8558 cellbender:remove-background: [epoch 029] average training loss: 2738.5300 cellbender:remove-background: [epoch 030] average training loss: 2743.5595 cellbender:remove-background: [epoch 030] average test loss: 2685.9626 cellbender:remove-background: [epoch 031] average training loss: 2770.4937 cellbender:remove-background: [epoch 032] average training loss: 2734.5400 cellbender:remove-background: [epoch 033] average training loss: 2743.8354 cellbender:remove-background: [epoch 034] average training loss: 2739.6133 cellbender:remove-background: [epoch 035] average training loss: 2737.9634 cellbender:remove-background: [epoch 035] average test loss: 2672.3308 cellbender:remove-background: [epoch 036] average training loss: 2749.5994 cellbender:remove-background: [epoch 037] average training loss: 2799.6746 cellbender:remove-background: [epoch 038] average training loss: 2782.7637 cellbender:remove-background: [epoch 039] average training loss: 2747.3575 cellbender:remove-background: [epoch 040] average training loss: 2823.1356 cellbender:remove-background: [epoch 040] average test loss: 2718.4492 cellbender:remove-background: [epoch 041] average training loss: 2763.8869 cellbender:remove-background: [epoch 042] average training loss: 2746.7681 cellbender:remove-background: [epoch 043] average training loss: 2823.7424 cellbender:remove-background: [epoch 044] average training loss: 2801.1956 cellbender:remove-background: [epoch 045] average training loss: 2770.4338 cellbender:remove-background: [epoch 045] average test loss: 2682.5153 cellbender:remove-background: [epoch 046] average training loss: 2841.5658 cellbender:remove-background: [epoch 047] average training loss: 2796.2585 cellbender:remove-background: [epoch 048] average training loss: 2804.3939 cellbender:remove-background: [epoch 049] average training loss: 2913.9935 cellbender:remove-background: [epoch 050] average training loss: 2831.9479 cellbender:remove-background: [epoch 050] average test loss: 2826.1773 cellbender:remove-background: [epoch 051] average training loss: 2803.0966 cellbender:remove-background: [epoch 052] average training loss: 2759.4664 cellbender:remove-background: [epoch 053] average training loss: 2804.5359 cellbender:remove-background: [epoch 054] average training loss: 2800.6795 cellbender:remove-background: [epoch 055] average training loss: 2842.5709 cellbender:remove-background: [epoch 055] average test loss: 2889.4186 cellbender:remove-background: [epoch 056] average training loss: 2890.9871 cellbender:remove-background: [epoch 057] average training loss: 2829.7507 cellbender:remove-background: [epoch 058] average training loss: 2800.6195 cellbender:remove-background: [epoch 059] average training loss: 2751.9475 cellbender:remove-background: [epoch 060] average training loss: 2768.2991 cellbender:remove-background: [epoch 060] average test loss: 2656.0151 cellbender:remove-background: [epoch 061] average training loss: 2832.2169 cellbender:remove-background: [epoch 062] average training loss: 2818.7473 cellbender:remove-background: [epoch 063] average training loss: 2776.3872 cellbender:remove-background: [epoch 064] average training loss: 2781.8709 cellbender:remove-background: [epoch 065] average training loss: 2779.3166 cellbender:remove-background: [epoch 065] average test loss: 2702.8991 cellbender:remove-background: [epoch 066] average training loss: 2787.5859 cellbender:remove-background: [epoch 067] average training loss: 2731.9928 cellbender:remove-background: [epoch 068] average training loss: 2805.8255 cellbender:remove-background: [epoch 069] average training loss: 2765.2010 cellbender:remove-background: [epoch 070] average training loss: 2731.1303 cellbender:remove-background: [epoch 070] average test loss: 2655.1970 cellbender:remove-background: [epoch 071] average training loss: 2797.1447 cellbender:remove-background: [epoch 072] average training loss: 2729.0957 cellbender:remove-background: [epoch 073] average training loss: 2782.2377 cellbender:remove-background: [epoch 074] average training loss: 2818.0096 cellbender:remove-background: [epoch 075] average training loss: 2730.7439 cellbender:remove-background: [epoch 075] average test loss: 2670.4115 cellbender:remove-background: [epoch 076] average training loss: 2765.3757 cellbender:remove-background: [epoch 077] average training loss: 2784.0514 cellbender:remove-background: [epoch 078] average training loss: 2755.1069 cellbender:remove-background: [epoch 079] average training loss: 2799.8896 cellbender:remove-background: [epoch 080] average training loss: 2787.1952 cellbender:remove-background: [epoch 080] average test loss: 2703.1764 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/1676-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 081] average training loss: 2729.5657 cellbender:remove-background: [epoch 082] average training loss: 2754.9627 cellbender:remove-background: [epoch 083] average training loss: 2751.2151 cellbender:remove-background: [epoch 084] average training loss: 2792.0576 cellbender:remove-background: [epoch 085] average training loss: 2748.9952 cellbender:remove-background: [epoch 085] average test loss: 2694.7707 cellbender:remove-background: [epoch 086] average training loss: 2729.7484 cellbender:remove-background: [epoch 087] average training loss: 2757.4055 cellbender:remove-background: [epoch 088] average training loss: 2807.4683 cellbender:remove-background: [epoch 089] average training loss: 2791.2707 cellbender:remove-background: [epoch 090] average training loss: 2770.8683 cellbender:remove-background: [epoch 090] average test loss: 2704.0169 cellbender:remove-background: [epoch 091] average training loss: 2765.8155 cellbender:remove-background: [epoch 092] average training loss: 2811.3418 cellbender:remove-background: [epoch 093] average training loss: 2784.6993 cellbender:remove-background: [epoch 094] average training loss: 2807.6013 cellbender:remove-background: [epoch 095] average training loss: 2749.1870 cellbender:remove-background: [epoch 095] average test loss: 2769.7355 cellbender:remove-background: [epoch 096] average training loss: 2821.1250 cellbender:remove-background: [epoch 097] average training loss: 2804.5361 cellbender:remove-background: [epoch 098] average training loss: 2757.5383 cellbender:remove-background: [epoch 099] average training loss: 2757.6556 cellbender:remove-background: [epoch 100] average training loss: 2779.9721 cellbender:remove-background: [epoch 100] average test loss: 2697.4966 cellbender:remove-background: [epoch 101] average training loss: 2767.8500 cellbender:remove-background: [epoch 102] average training loss: 2750.3368 cellbender:remove-background: [epoch 103] average training loss: 2751.7885 cellbender:remove-background: [epoch 104] average training loss: 2808.0537 cellbender:remove-background: [epoch 105] average training loss: 2793.6472 cellbender:remove-background: [epoch 105] average test loss: 2690.5691 cellbender:remove-background: [epoch 106] average training loss: 2779.3640 cellbender:remove-background: [epoch 107] average training loss: 2783.0342 cellbender:remove-background: [epoch 108] average training loss: 2795.4842 cellbender:remove-background: [epoch 109] average training loss: 2805.7021 cellbender:remove-background: [epoch 110] average training loss: 2777.6604 cellbender:remove-background: [epoch 110] average test loss: 2707.3213 cellbender:remove-background: [epoch 111] average training loss: 2807.3424 cellbender:remove-background: [epoch 112] average training loss: 2818.8501 cellbender:remove-background: [epoch 113] average training loss: 2810.6675 cellbender:remove-background: [epoch 114] average training loss: 2795.4991 cellbender:remove-background: [epoch 115] average training loss: 2738.2841 cellbender:remove-background: [epoch 115] average test loss: 2732.9702 cellbender:remove-background: [epoch 116] average training loss: 2769.5329 cellbender:remove-background: [epoch 117] average training loss: 2784.9920 cellbender:remove-background: [epoch 118] average training loss: 2775.8960 cellbender:remove-background: [epoch 119] average training loss: 2799.3212 cellbender:remove-background: [epoch 120] average training loss: 2764.2657 cellbender:remove-background: [epoch 120] average test loss: 2730.3755 cellbender:remove-background: [epoch 121] average training loss: 2880.6532 cellbender:remove-background: [epoch 122] average training loss: 2751.2919 cellbender:remove-background: [epoch 123] average training loss: 2807.0107 cellbender:remove-background: [epoch 124] average training loss: 2803.2186 cellbender:remove-background: [epoch 125] average training loss: 2766.8311 cellbender:remove-background: [epoch 125] average test loss: 2738.2769 cellbender:remove-background: [epoch 126] average training loss: 2853.9398 cellbender:remove-background: [epoch 127] average training loss: 2811.0231 cellbender:remove-background: [epoch 128] average training loss: 2739.4596 cellbender:remove-background: [epoch 129] average training loss: 2776.1320 cellbender:remove-background: [epoch 130] average training loss: 2809.9384 cellbender:remove-background: [epoch 130] average test loss: 2802.4701 cellbender:remove-background: [epoch 131] average training loss: 2828.2840 cellbender:remove-background: [epoch 132] average training loss: 2798.1989 cellbender:remove-background: [epoch 133] average training loss: 2790.7684 cellbender:remove-background: [epoch 134] average training loss: 2778.8591 cellbender:remove-background: [epoch 135] average training loss: 2770.8458 cellbender:remove-background: [epoch 135] average test loss: 2756.6684 cellbender:remove-background: [epoch 136] average training loss: 2773.8192 cellbender:remove-background: [epoch 137] average training loss: 2786.1192 cellbender:remove-background: [epoch 138] average training loss: 2789.4676 cellbender:remove-background: [epoch 139] average training loss: 2796.1008 cellbender:remove-background: [epoch 140] average training loss: 2760.9359 cellbender:remove-background: [epoch 140] average test loss: 2712.5023 cellbender:remove-background: [epoch 141] average training loss: 2803.5011 cellbender:remove-background: [epoch 142] average training loss: 2758.7538 cellbender:remove-background: [epoch 143] average training loss: 2762.1506 cellbender:remove-background: [epoch 144] average training loss: 2773.3608 cellbender:remove-background: [epoch 145] average training loss: 2761.2272 cellbender:remove-background: [epoch 145] average test loss: 2719.0603 cellbender:remove-background: [epoch 146] average training loss: 2757.7498 cellbender:remove-background: [epoch 147] average training loss: 2781.2333 cellbender:remove-background: [epoch 148] average training loss: 2756.0409 cellbender:remove-background: [epoch 149] average training loss: 2761.3931 cellbender:remove-background: [epoch 150] average training loss: 2768.8402 cellbender:remove-background: [epoch 150] average test loss: 2697.5930 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/1676-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:52:20 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp1rc6ebb7 cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp1rc6ebb7 /tmp/tmp1rc6ebb7/3e2e5bdedb_random.pyro /tmp/tmp1rc6ebb7/3e2e5bdedb_random.cuda /tmp/tmp1rc6ebb7/3e2e5bdedb_model.torch /tmp/tmp1rc6ebb7/3e2e5bdedb_optim.torch /tmp/tmp1rc6ebb7/3e2e5bdedb_optim.pyro /tmp/tmp1rc6ebb7/3e2e5bdedb_params.pyro /tmp/tmp1rc6ebb7/3e2e5bdedb_train.loaderstate /tmp/tmp1rc6ebb7/3e2e5bdedb_test.loaderstate /tmp/tmp1rc6ebb7/3e2e5bdedb_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 (1/61) cellbender:remove-background: [0.02 mins per chunk] cellbender:remove-background: Working on chunk (2/61) cellbender:remove-background: Working on chunk (3/61) cellbender:remove-background: Working on chunk (4/61) cellbender:remove-background: Working on chunk (5/61) cellbender:remove-background: Working on chunk (6/61) cellbender:remove-background: Working on chunk (7/61) cellbender:remove-background: Working on chunk (8/61) cellbender:remove-background: Working on chunk (9/61) cellbender:remove-background: Working on chunk (10/61) cellbender:remove-background: Working on chunk (11/61) cellbender:remove-background: Working on chunk (12/61) cellbender:remove-background: Working on chunk (13/61) cellbender:remove-background: Working on chunk (14/61) cellbender:remove-background: Working on chunk (15/61) cellbender:remove-background: Working on chunk (16/61) cellbender:remove-background: Working on chunk (17/61) cellbender:remove-background: Working on chunk (18/61) cellbender:remove-background: Working on chunk (19/61) cellbender:remove-background: Working on chunk (20/61) cellbender:remove-background: Working on chunk (21/61) cellbender:remove-background: Working on chunk (22/61) cellbender:remove-background: Working on chunk (23/61) cellbender:remove-background: Working on chunk (24/61) cellbender:remove-background: Working on chunk (25/61) cellbender:remove-background: Working on chunk (26/61) cellbender:remove-background: Working on chunk (27/61) cellbender:remove-background: Working on chunk (28/61) cellbender:remove-background: Working on chunk (29/61) cellbender:remove-background: Working on chunk (30/61) cellbender:remove-background: Working on chunk (31/61) cellbender:remove-background: Working on chunk (32/61) cellbender:remove-background: Working on chunk (33/61) cellbender:remove-background: Working on chunk (34/61) cellbender:remove-background: Working on chunk (35/61) cellbender:remove-background: Working on chunk (36/61) cellbender:remove-background: Working on chunk (37/61) cellbender:remove-background: Working on chunk (38/61) cellbender:remove-background: Working on chunk (39/61) cellbender:remove-background: Working on chunk (40/61) cellbender:remove-background: Working on chunk (41/61) cellbender:remove-background: Working on chunk (42/61) cellbender:remove-background: Working on chunk (43/61) cellbender:remove-background: Working on chunk (44/61) cellbender:remove-background: Working on chunk (45/61) cellbender:remove-background: Working on chunk (46/61) cellbender:remove-background: Working on chunk (47/61) cellbender:remove-background: Working on chunk (48/61) cellbender:remove-background: Working on chunk (49/61) cellbender:remove-background: Working on chunk (50/61) cellbender:remove-background: Working on chunk (51/61) cellbender:remove-background: Working on chunk (52/61) cellbender:remove-background: Working on chunk (53/61) cellbender:remove-background: Working on chunk (54/61) cellbender:remove-background: Working on chunk (55/61) cellbender:remove-background: Working on chunk (56/61) cellbender:remove-background: Working on chunk (57/61) cellbender:remove-background: Working on chunk (58/61) cellbender:remove-background: Working on chunk (59/61) cellbender:remove-background: Working on chunk (60/61) cellbender:remove-background: Working on chunk (61/61) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1676-Schizophrenia-DLPFC/1676-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/1676-Schizophrenia-DLPFC/1676-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:55:59 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1676-Schizophrenia-DLPFC/1676-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/1676-Schizophrenia-DLPFC/1676-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: [1.87 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 16:09:36 Total MCKP estimation time = 787.52 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/1676-Schizophrenia-DLPFC/1676-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/1676-Schizophrenia-DLPFC/1676-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/1676-Schizophrenia-DLPFC/1676-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/1676-Schizophrenia-DLPFC/1676-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:09:56