cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1527-Schizophrenia-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1527-Schizophrenia-DLPFC/1527-Schizophrenia-DLPFC.cellbender.output.h5 --cuda --expected-cells 6568 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash a540ac1271) cellbender:remove-background: 2024-06-06 15:20:32 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/1527-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: 32519 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 7406 cellbender:remove-background: Prior on counts for empty droplets is 58 cellbender:remove-background: Excluding 12271 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 20248 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 29 cellbender:remove-background: Using 6568 probable cell barcodes, plus an additional 13432 barcodes, and 43056 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 58 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpmomn08bz 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: 7835.3054 cellbender:remove-background: [epoch 002] average training loss: 5572.3273 (6.2 seconds per epoch) cellbender:remove-background: Will checkpoint every 68 epochs cellbender:remove-background: [epoch 003] average training loss: 4314.6584 cellbender:remove-background: [epoch 004] average training loss: 3804.1112 cellbender:remove-background: [epoch 005] average training loss: 3657.9975 cellbender:remove-background: [epoch 005] average test loss: 3640.8232 cellbender:remove-background: [epoch 006] average training loss: 3615.3279 cellbender:remove-background: [epoch 007] average training loss: 3570.4758 cellbender:remove-background: [epoch 008] average training loss: 3541.8742 cellbender:remove-background: [epoch 009] average training loss: 3530.7034 cellbender:remove-background: [epoch 010] average training loss: 3481.0074 cellbender:remove-background: [epoch 010] average test loss: 3425.3288 cellbender:remove-background: [epoch 011] average training loss: 3388.1531 cellbender:remove-background: [epoch 012] average training loss: 3284.4220 cellbender:remove-background: [epoch 013] average training loss: 3253.8459 cellbender:remove-background: [epoch 014] average training loss: 3262.8508 cellbender:remove-background: [epoch 015] average training loss: 3236.1592 cellbender:remove-background: [epoch 015] average test loss: 3227.9208 cellbender:remove-background: [epoch 016] average training loss: 3224.6103 cellbender:remove-background: [epoch 017] average training loss: 3235.6077 cellbender:remove-background: [epoch 018] average training loss: 3221.7872 cellbender:remove-background: [epoch 019] average training loss: 3211.8989 cellbender:remove-background: [epoch 020] average training loss: 3191.4811 cellbender:remove-background: [epoch 020] average test loss: 3172.1609 cellbender:remove-background: [epoch 021] average training loss: 3186.4672 cellbender:remove-background: [epoch 022] average training loss: 3161.3243 cellbender:remove-background: [epoch 023] average training loss: 3137.8070 cellbender:remove-background: [epoch 024] average training loss: 3116.5478 cellbender:remove-background: [epoch 025] average training loss: 3106.5758 cellbender:remove-background: [epoch 025] average test loss: 3058.4186 cellbender:remove-background: [epoch 026] average training loss: 3092.6744 cellbender:remove-background: [epoch 027] average training loss: 3086.8660 cellbender:remove-background: [epoch 028] average training loss: 3084.7826 cellbender:remove-background: [epoch 029] average training loss: 3075.8148 cellbender:remove-background: [epoch 030] average training loss: 3071.5502 cellbender:remove-background: [epoch 030] average test loss: 3020.4821 cellbender:remove-background: [epoch 031] average training loss: 3066.7587 cellbender:remove-background: [epoch 032] average training loss: 3061.7071 cellbender:remove-background: [epoch 033] average training loss: 3059.8499 cellbender:remove-background: [epoch 034] average training loss: 3056.4965 cellbender:remove-background: [epoch 035] average training loss: 3052.5574 cellbender:remove-background: [epoch 035] average test loss: 2991.8952 cellbender:remove-background: [epoch 036] average training loss: 3050.5153 cellbender:remove-background: [epoch 037] average training loss: 3047.0389 cellbender:remove-background: [epoch 038] average training loss: 3043.4354 cellbender:remove-background: [epoch 039] average training loss: 3039.9432 cellbender:remove-background: [epoch 040] average training loss: 3038.2529 cellbender:remove-background: [epoch 040] average test loss: 2967.7633 cellbender:remove-background: [epoch 041] average training loss: 3039.3402 cellbender:remove-background: [epoch 042] average training loss: 3036.4094 cellbender:remove-background: [epoch 043] average training loss: 3033.0046 cellbender:remove-background: [epoch 044] average training loss: 3033.7851 cellbender:remove-background: [epoch 045] average training loss: 3032.4825 cellbender:remove-background: [epoch 045] average test loss: 2966.4461 cellbender:remove-background: [epoch 046] average training loss: 3032.9978 cellbender:remove-background: [epoch 047] average training loss: 3027.2258 cellbender:remove-background: [epoch 048] average training loss: 3026.3198 cellbender:remove-background: [epoch 049] average training loss: 3024.2363 cellbender:remove-background: [epoch 050] average training loss: 3026.1041 cellbender:remove-background: [epoch 050] average test loss: 2964.0032 cellbender:remove-background: [epoch 051] average training loss: 3029.1419 cellbender:remove-background: [epoch 052] average training loss: 3019.3252 cellbender:remove-background: [epoch 053] average training loss: 3028.1171 cellbender:remove-background: [epoch 054] average training loss: 3028.9778 cellbender:remove-background: [epoch 055] average training loss: 3024.9169 cellbender:remove-background: [epoch 055] average test loss: 2955.0149 cellbender:remove-background: [epoch 056] average training loss: 3022.1136 cellbender:remove-background: [epoch 057] average training loss: 3049.2848 cellbender:remove-background: [epoch 058] average training loss: 3039.1821 cellbender:remove-background: [epoch 059] average training loss: 3041.3337 cellbender:remove-background: [epoch 060] average training loss: 3026.6366 cellbender:remove-background: [epoch 060] average test loss: 2953.4193 cellbender:remove-background: [epoch 061] average training loss: 3018.9713 cellbender:remove-background: [epoch 062] average training loss: 3039.6237 cellbender:remove-background: [epoch 063] average training loss: 3022.4360 cellbender:remove-background: [epoch 064] average training loss: 3009.4231 cellbender:remove-background: [epoch 065] average training loss: 3015.6120 cellbender:remove-background: [epoch 065] average test loss: 2962.0811 cellbender:remove-background: [epoch 066] average training loss: 3018.1069 cellbender:remove-background: [epoch 067] average training loss: 3012.2548 cellbender:remove-background: [epoch 068] average training loss: 3012.8253 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/1527-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 069] average training loss: 3005.9182 cellbender:remove-background: [epoch 070] average training loss: 3006.6263 cellbender:remove-background: [epoch 070] average test loss: 2988.2504 cellbender:remove-background: [epoch 071] average training loss: 3009.9482 cellbender:remove-background: [epoch 072] average training loss: 3012.7213 cellbender:remove-background: [epoch 073] average training loss: 3006.9825 cellbender:remove-background: [epoch 074] average training loss: 3006.5743 cellbender:remove-background: [epoch 075] average training loss: 3008.7482 cellbender:remove-background: [epoch 075] average test loss: 2963.0195 cellbender:remove-background: [epoch 076] average training loss: 3004.1787 cellbender:remove-background: [epoch 077] average training loss: 3003.4031 cellbender:remove-background: [epoch 078] average training loss: 3006.7789 cellbender:remove-background: [epoch 079] average training loss: 3006.2176 cellbender:remove-background: [epoch 080] average training loss: 3002.2303 cellbender:remove-background: [epoch 080] average test loss: 2951.0903 cellbender:remove-background: [epoch 081] average training loss: 3001.1725 cellbender:remove-background: [epoch 082] average training loss: 3004.3645 cellbender:remove-background: [epoch 083] average training loss: 3000.1625 cellbender:remove-background: [epoch 084] average training loss: 3000.4602 cellbender:remove-background: [epoch 085] average training loss: 2999.1309 cellbender:remove-background: [epoch 085] average test loss: 2951.0870 cellbender:remove-background: [epoch 086] average training loss: 2996.8254 cellbender:remove-background: [epoch 087] average training loss: 2995.5660 cellbender:remove-background: [epoch 088] average training loss: 2997.6739 cellbender:remove-background: [epoch 089] average training loss: 2995.5414 cellbender:remove-background: [epoch 090] average training loss: 2994.9945 cellbender:remove-background: [epoch 090] average test loss: 2943.7911 cellbender:remove-background: [epoch 091] average training loss: 2992.9186 cellbender:remove-background: [epoch 092] average training loss: 2995.0956 cellbender:remove-background: [epoch 093] average training loss: 2994.1361 cellbender:remove-background: [epoch 094] average training loss: 2992.4274 cellbender:remove-background: [epoch 095] average training loss: 2995.6697 cellbender:remove-background: [epoch 095] average test loss: 2954.2992 cellbender:remove-background: [epoch 096] average training loss: 2995.6654 cellbender:remove-background: [epoch 097] average training loss: 2995.7693 cellbender:remove-background: [epoch 098] average training loss: 2993.1332 cellbender:remove-background: [epoch 099] average training loss: 2996.2971 cellbender:remove-background: [epoch 100] average training loss: 2993.0306 cellbender:remove-background: [epoch 100] average test loss: 2959.5416 cellbender:remove-background: [epoch 101] average training loss: 2989.6025 cellbender:remove-background: [epoch 102] average training loss: 2990.5437 cellbender:remove-background: [epoch 103] average training loss: 2991.1112 cellbender:remove-background: [epoch 104] average training loss: 2989.7001 cellbender:remove-background: [epoch 105] average training loss: 2992.2912 cellbender:remove-background: [epoch 105] average test loss: 2938.7779 cellbender:remove-background: [epoch 106] average training loss: 2988.7554 cellbender:remove-background: [epoch 107] average training loss: 2990.3734 cellbender:remove-background: [epoch 108] average training loss: 2991.6990 cellbender:remove-background: [epoch 109] average training loss: 2992.3557 cellbender:remove-background: [epoch 110] average training loss: 2989.2938 cellbender:remove-background: [epoch 110] average test loss: 2963.0493 cellbender:remove-background: [epoch 111] average training loss: 2990.6674 cellbender:remove-background: [epoch 112] average training loss: 2989.1034 cellbender:remove-background: [epoch 113] average training loss: 2988.1531 cellbender:remove-background: [epoch 114] average training loss: 2987.5799 cellbender:remove-background: [epoch 115] average training loss: 2988.1497 cellbender:remove-background: [epoch 115] average test loss: 2943.8769 cellbender:remove-background: [epoch 116] average training loss: 2985.6422 cellbender:remove-background: [epoch 117] average training loss: 2985.9195 cellbender:remove-background: [epoch 118] average training loss: 2986.8328 cellbender:remove-background: [epoch 119] average training loss: 2986.9965 cellbender:remove-background: [epoch 120] average training loss: 2985.6944 cellbender:remove-background: [epoch 120] average test loss: 2947.5187 cellbender:remove-background: [epoch 121] average training loss: 2989.8182 cellbender:remove-background: [epoch 122] average training loss: 2983.8537 cellbender:remove-background: [epoch 123] average training loss: 2984.4312 cellbender:remove-background: [epoch 124] average training loss: 2984.3841 cellbender:remove-background: [epoch 125] average training loss: 2984.7618 cellbender:remove-background: [epoch 125] average test loss: 2946.4930 cellbender:remove-background: [epoch 126] average training loss: 2985.4218 cellbender:remove-background: [epoch 127] average training loss: 2984.1841 cellbender:remove-background: [epoch 128] average training loss: 2984.2469 cellbender:remove-background: [epoch 129] average training loss: 2982.5746 cellbender:remove-background: [epoch 130] average training loss: 2984.3335 cellbender:remove-background: [epoch 130] average test loss: 2946.7553 cellbender:remove-background: [epoch 131] average training loss: 2983.8997 cellbender:remove-background: [epoch 132] average training loss: 2984.0524 cellbender:remove-background: [epoch 133] average training loss: 2982.9269 cellbender:remove-background: [epoch 134] average training loss: 2984.0319 cellbender:remove-background: [epoch 135] average training loss: 2983.4853 cellbender:remove-background: [epoch 135] average test loss: 2942.5757 cellbender:remove-background: [epoch 136] average training loss: 2982.9931 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/1527-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: [epoch 137] average training loss: 2982.8785 cellbender:remove-background: [epoch 138] average training loss: 2984.1900 cellbender:remove-background: [epoch 139] average training loss: 2982.9258 cellbender:remove-background: [epoch 140] average training loss: 2980.3698 cellbender:remove-background: [epoch 140] average test loss: 2939.0537 cellbender:remove-background: [epoch 141] average training loss: 2980.4624 cellbender:remove-background: [epoch 142] average training loss: 2983.3574 cellbender:remove-background: [epoch 143] average training loss: 2983.1978 cellbender:remove-background: [epoch 144] average training loss: 2982.8129 cellbender:remove-background: [epoch 145] average training loss: 2981.6313 cellbender:remove-background: [epoch 145] average test loss: 2942.8897 cellbender:remove-background: [epoch 146] average training loss: 2982.8558 cellbender:remove-background: [epoch 147] average training loss: 2981.7183 cellbender:remove-background: [epoch 148] average training loss: 2983.1647 cellbender:remove-background: [epoch 149] average training loss: 2982.0644 cellbender:remove-background: [epoch 150] average training loss: 2982.1337 cellbender:remove-background: [epoch 150] average test loss: 2943.8039 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/1527-Schizophrenia-DLPFC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:38:44 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpx0n1x3is cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpx0n1x3is /tmp/tmpx0n1x3is/a540ac1271_random.pyro /tmp/tmpx0n1x3is/a540ac1271_random.cuda /tmp/tmpx0n1x3is/a540ac1271_model.torch /tmp/tmpx0n1x3is/a540ac1271_optim.torch /tmp/tmpx0n1x3is/a540ac1271_optim.pyro /tmp/tmpx0n1x3is/a540ac1271_params.pyro /tmp/tmpx0n1x3is/a540ac1271_train.loaderstate /tmp/tmpx0n1x3is/a540ac1271_test.loaderstate /tmp/tmpx0n1x3is/a540ac1271_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 (1/55) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/55) cellbender:remove-background: Working on chunk (3/55) cellbender:remove-background: Working on chunk (4/55) cellbender:remove-background: Working on chunk (5/55) cellbender:remove-background: Working on chunk (6/55) cellbender:remove-background: Working on chunk (7/55) cellbender:remove-background: Working on chunk (8/55) cellbender:remove-background: Working on chunk (9/55) cellbender:remove-background: Working on chunk (10/55) cellbender:remove-background: Working on chunk (11/55) cellbender:remove-background: Working on chunk (12/55) cellbender:remove-background: Working on chunk (13/55) cellbender:remove-background: Working on chunk (14/55) cellbender:remove-background: Working on chunk (15/55) cellbender:remove-background: Working on chunk (16/55) cellbender:remove-background: Working on chunk (17/55) cellbender:remove-background: Working on chunk (18/55) cellbender:remove-background: Working on chunk (19/55) cellbender:remove-background: Working on chunk (20/55) cellbender:remove-background: Working on chunk (21/55) cellbender:remove-background: Working on chunk (22/55) cellbender:remove-background: Working on chunk (23/55) cellbender:remove-background: Working on chunk (24/55) cellbender:remove-background: Working on chunk (25/55) cellbender:remove-background: Working on chunk (26/55) cellbender:remove-background: Working on chunk (27/55) cellbender:remove-background: Working on chunk (28/55) cellbender:remove-background: Working on chunk (29/55) cellbender:remove-background: Working on chunk (30/55) cellbender:remove-background: Working on chunk (31/55) cellbender:remove-background: Working on chunk (32/55) cellbender:remove-background: Working on chunk (33/55) cellbender:remove-background: Working on chunk (34/55) cellbender:remove-background: Working on chunk (35/55) cellbender:remove-background: Working on chunk (36/55) cellbender:remove-background: Working on chunk (37/55) cellbender:remove-background: Working on chunk (38/55) cellbender:remove-background: Working on chunk (39/55) cellbender:remove-background: Working on chunk (40/55) cellbender:remove-background: Working on chunk (41/55) cellbender:remove-background: Working on chunk (42/55) cellbender:remove-background: Working on chunk (43/55) cellbender:remove-background: Working on chunk (44/55) cellbender:remove-background: Working on chunk (45/55) cellbender:remove-background: Working on chunk (46/55) cellbender:remove-background: Working on chunk (47/55) cellbender:remove-background: Working on chunk (48/55) cellbender:remove-background: Working on chunk (49/55) cellbender:remove-background: Working on chunk (50/55) cellbender:remove-background: Working on chunk (51/55) cellbender:remove-background: Working on chunk (52/55) cellbender:remove-background: Working on chunk (53/55) cellbender:remove-background: Working on chunk (54/55) cellbender:remove-background: Working on chunk (55/55) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1527-Schizophrenia-DLPFC/1527-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/1527-Schizophrenia-DLPFC/1527-Schizophrenia-DLPFC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:42:20 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1527-Schizophrenia-DLPFC/1527-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/1527-Schizophrenia-DLPFC/1527-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: [1.57 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 15:53:46 Total MCKP estimation time = 643.83 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/1527-Schizophrenia-DLPFC/1527-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/1527-Schizophrenia-DLPFC/1527-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/1527-Schizophrenia-DLPFC/1527-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/1527-Schizophrenia-DLPFC/1527-Schizophrenia-DLPFC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:54:04