cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1527-Schizophrenia-dACC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1527-Schizophrenia-dACC/1527-Schizophrenia-dACC.cellbender.output.h5 --cuda --expected-cells 5015 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 32fc3f2579) cellbender:remove-background: 2024-06-06 15:15:02 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-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: 31936 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 4870 cellbender:remove-background: Prior on counts for empty droplets is 85 cellbender:remove-background: Excluding 10130 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21806 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 42 cellbender:remove-background: Using 5015 probable cell barcodes, plus an additional 14985 barcodes, and 43919 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 85 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmplac5qalv 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: 4914.7409 cellbender:remove-background: [epoch 002] average training loss: 3835.1816 (6.3 seconds per epoch) cellbender:remove-background: Will checkpoint every 68 epochs cellbender:remove-background: [epoch 003] average training loss: 3290.9771 cellbender:remove-background: [epoch 004] average training loss: 2951.1248 cellbender:remove-background: [epoch 005] average training loss: 2871.7648 cellbender:remove-background: [epoch 005] average test loss: 2967.8124 cellbender:remove-background: [epoch 006] average training loss: 2837.0521 cellbender:remove-background: [epoch 007] average training loss: 2807.4745 cellbender:remove-background: [epoch 008] average training loss: 2772.6750 cellbender:remove-background: [epoch 009] average training loss: 2754.9708 cellbender:remove-background: [epoch 010] average training loss: 2651.9126 cellbender:remove-background: [epoch 010] average test loss: 2695.5414 cellbender:remove-background: [epoch 011] average training loss: 2605.4376 cellbender:remove-background: [epoch 012] average training loss: 2577.4746 cellbender:remove-background: [epoch 013] average training loss: 2556.8205 cellbender:remove-background: [epoch 014] average training loss: 2569.7164 cellbender:remove-background: [epoch 015] average training loss: 2545.0953 cellbender:remove-background: [epoch 015] average test loss: 2576.3429 cellbender:remove-background: [epoch 016] average training loss: 2535.6970 cellbender:remove-background: [epoch 017] average training loss: 2542.3761 cellbender:remove-background: [epoch 018] average training loss: 2527.4059 cellbender:remove-background: [epoch 019] average training loss: 2518.8651 cellbender:remove-background: [epoch 020] average training loss: 2497.6395 cellbender:remove-background: [epoch 020] average test loss: 2520.3124 cellbender:remove-background: [epoch 021] average training loss: 2473.1623 cellbender:remove-background: [epoch 022] average training loss: 2460.8708 cellbender:remove-background: [epoch 023] average training loss: 2456.5190 cellbender:remove-background: [epoch 024] average training loss: 2435.1159 cellbender:remove-background: [epoch 025] average training loss: 2427.1028 cellbender:remove-background: [epoch 025] average test loss: 2425.0166 cellbender:remove-background: [epoch 026] average training loss: 2411.2907 cellbender:remove-background: [epoch 027] average training loss: 2404.6744 cellbender:remove-background: [epoch 028] average training loss: 2402.6073 cellbender:remove-background: [epoch 029] average training loss: 2393.8254 cellbender:remove-background: [epoch 030] average training loss: 2386.3693 cellbender:remove-background: [epoch 030] average test loss: 2378.0048 cellbender:remove-background: [epoch 031] average training loss: 2382.6456 cellbender:remove-background: [epoch 032] average training loss: 2377.4927 cellbender:remove-background: [epoch 033] average training loss: 2376.5152 cellbender:remove-background: [epoch 034] average training loss: 2375.6805 cellbender:remove-background: [epoch 035] average training loss: 2371.6301 cellbender:remove-background: [epoch 035] average test loss: 2376.9494 cellbender:remove-background: [epoch 036] average training loss: 2371.2088 cellbender:remove-background: [epoch 037] average training loss: 2370.0434 cellbender:remove-background: [epoch 038] average training loss: 2372.0622 cellbender:remove-background: [epoch 039] average training loss: 2379.2415 cellbender:remove-background: [epoch 040] average training loss: 2378.5948 cellbender:remove-background: [epoch 040] average test loss: 2386.1971 cellbender:remove-background: [epoch 041] average training loss: 2386.4352 cellbender:remove-background: [epoch 042] average training loss: 2394.1302 cellbender:remove-background: [epoch 043] average training loss: 2394.2958 cellbender:remove-background: [epoch 044] average training loss: 2394.8877 cellbender:remove-background: [epoch 045] average training loss: 2391.1322 cellbender:remove-background: [epoch 045] average test loss: 2392.5914 cellbender:remove-background: [epoch 046] average training loss: 2387.4383 cellbender:remove-background: [epoch 047] average training loss: 2409.8320 cellbender:remove-background: [epoch 048] average training loss: 2399.3616 cellbender:remove-background: [epoch 049] average training loss: 2398.7347 cellbender:remove-background: [epoch 050] average training loss: 2419.0487 cellbender:remove-background: [epoch 050] average test loss: 2415.4693 cellbender:remove-background: [epoch 051] average training loss: 2417.6091 cellbender:remove-background: [epoch 052] average training loss: 2411.2988 cellbender:remove-background: [epoch 053] average training loss: 2404.2734 cellbender:remove-background: [epoch 054] average training loss: 2417.8910 cellbender:remove-background: [epoch 055] average training loss: 2407.8862 cellbender:remove-background: [epoch 055] average test loss: 2378.3273 cellbender:remove-background: [epoch 056] average training loss: 2391.6947 cellbender:remove-background: [epoch 057] average training loss: 2398.0486 cellbender:remove-background: [epoch 058] average training loss: 2391.0230 cellbender:remove-background: [epoch 059] average training loss: 2397.0850 cellbender:remove-background: [epoch 060] average training loss: 2402.1518 cellbender:remove-background: [epoch 060] average test loss: 2398.2729 cellbender:remove-background: [epoch 061] average training loss: 2408.5967 cellbender:remove-background: [epoch 062] average training loss: 2407.4266 cellbender:remove-background: [epoch 063] average training loss: 2408.6504 cellbender:remove-background: [epoch 064] average training loss: 2395.3627 cellbender:remove-background: [epoch 065] average training loss: 2393.4465 cellbender:remove-background: [epoch 065] average test loss: 2433.7787 cellbender:remove-background: [epoch 066] average training loss: 2392.1228 cellbender:remove-background: [epoch 067] average training loss: 2396.0334 cellbender:remove-background: [epoch 068] average training loss: 2389.9756 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-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 069] average training loss: 2404.0070 cellbender:remove-background: [epoch 070] average training loss: 2394.4187 cellbender:remove-background: [epoch 070] average test loss: 2402.8009 cellbender:remove-background: [epoch 071] average training loss: 2384.0734 cellbender:remove-background: [epoch 072] average training loss: 2387.8762 cellbender:remove-background: [epoch 073] average training loss: 2377.3657 cellbender:remove-background: [epoch 074] average training loss: 2380.3317 cellbender:remove-background: [epoch 075] average training loss: 2382.1563 cellbender:remove-background: [epoch 075] average test loss: 2398.5564 cellbender:remove-background: [epoch 076] average training loss: 2394.3398 cellbender:remove-background: [epoch 077] average training loss: 2386.7311 cellbender:remove-background: [epoch 078] average training loss: 2383.6192 cellbender:remove-background: [epoch 079] average training loss: 2381.0675 cellbender:remove-background: [epoch 080] average training loss: 2385.2512 cellbender:remove-background: [epoch 080] average test loss: 2387.6616 cellbender:remove-background: [epoch 081] average training loss: 2383.9064 cellbender:remove-background: [epoch 082] average training loss: 2384.7284 cellbender:remove-background: [epoch 083] average training loss: 2372.5999 cellbender:remove-background: [epoch 084] average training loss: 2376.1926 cellbender:remove-background: [epoch 085] average training loss: 2386.2462 cellbender:remove-background: [epoch 085] average test loss: 2390.1043 cellbender:remove-background: [epoch 086] average training loss: 2387.8474 cellbender:remove-background: [epoch 087] average training loss: 2378.1180 cellbender:remove-background: [epoch 088] average training loss: 2380.1960 cellbender:remove-background: [epoch 089] average training loss: 2380.2650 cellbender:remove-background: [epoch 090] average training loss: 2375.4229 cellbender:remove-background: [epoch 090] average test loss: 2420.2964 cellbender:remove-background: [epoch 091] average training loss: 2372.8287 cellbender:remove-background: [epoch 092] average training loss: 2373.9258 cellbender:remove-background: [epoch 093] average training loss: 2381.5104 cellbender:remove-background: [epoch 094] average training loss: 2371.2927 cellbender:remove-background: [epoch 095] average training loss: 2371.7466 cellbender:remove-background: [epoch 095] average test loss: 2399.1535 cellbender:remove-background: [epoch 096] average training loss: 2367.7448 cellbender:remove-background: [epoch 097] average training loss: 2377.9925 cellbender:remove-background: [epoch 098] average training loss: 2377.1765 cellbender:remove-background: [epoch 099] average training loss: 2376.1602 cellbender:remove-background: [epoch 100] average training loss: 2373.2905 cellbender:remove-background: [epoch 100] average test loss: 2380.9825 cellbender:remove-background: [epoch 101] average training loss: 2370.2087 cellbender:remove-background: [epoch 102] average training loss: 2361.2182 cellbender:remove-background: [epoch 103] average training loss: 2371.2759 cellbender:remove-background: [epoch 104] average training loss: 2379.3415 cellbender:remove-background: [epoch 105] average training loss: 2370.3605 cellbender:remove-background: [epoch 105] average test loss: 2402.9141 cellbender:remove-background: [epoch 106] average training loss: 2381.2720 cellbender:remove-background: [epoch 107] average training loss: 2368.6449 cellbender:remove-background: [epoch 108] average training loss: 2363.0053 cellbender:remove-background: [epoch 109] average training loss: 2366.3325 cellbender:remove-background: [epoch 110] average training loss: 2384.7520 cellbender:remove-background: [epoch 110] average test loss: 2400.3889 cellbender:remove-background: [epoch 111] average training loss: 2365.6634 cellbender:remove-background: [epoch 112] average training loss: 2369.4493 cellbender:remove-background: [epoch 113] average training loss: 2367.6557 cellbender:remove-background: [epoch 114] average training loss: 2368.0195 cellbender:remove-background: [epoch 115] average training loss: 2362.5121 cellbender:remove-background: [epoch 115] average test loss: 2412.6607 cellbender:remove-background: [epoch 116] average training loss: 2363.8331 cellbender:remove-background: [epoch 117] average training loss: 2365.7027 cellbender:remove-background: [epoch 118] average training loss: 2360.4579 cellbender:remove-background: [epoch 119] average training loss: 2361.2797 cellbender:remove-background: [epoch 120] average training loss: 2379.2994 cellbender:remove-background: [epoch 120] average test loss: 2386.9161 cellbender:remove-background: [epoch 121] average training loss: 2361.5969 cellbender:remove-background: [epoch 122] average training loss: 2363.8584 cellbender:remove-background: [epoch 123] average training loss: 2363.7814 cellbender:remove-background: [epoch 124] average training loss: 2361.9580 cellbender:remove-background: [epoch 125] average training loss: 2359.0371 cellbender:remove-background: [epoch 125] average test loss: 2407.1802 cellbender:remove-background: [epoch 126] average training loss: 2362.5530 cellbender:remove-background: [epoch 127] average training loss: 2367.1504 cellbender:remove-background: [epoch 128] average training loss: 2376.6509 cellbender:remove-background: [epoch 129] average training loss: 2360.5855 cellbender:remove-background: [epoch 130] average training loss: 2361.1249 cellbender:remove-background: [epoch 130] average test loss: 2394.9823 cellbender:remove-background: [epoch 131] average training loss: 2360.8579 cellbender:remove-background: [epoch 132] average training loss: 2363.9831 cellbender:remove-background: [epoch 133] average training loss: 2357.3232 cellbender:remove-background: [epoch 134] average training loss: 2357.8254 cellbender:remove-background: [epoch 135] average training loss: 2357.4067 cellbender:remove-background: [epoch 135] average test loss: 2395.5751 cellbender:remove-background: [epoch 136] average training loss: 2362.0042 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-dACC/ckpt.tar.gz cellbender:remove-background: [epoch 137] average training loss: 2362.1404 cellbender:remove-background: [epoch 138] average training loss: 2365.3281 cellbender:remove-background: [epoch 139] average training loss: 2355.5294 cellbender:remove-background: [epoch 140] average training loss: 2364.8148 cellbender:remove-background: [epoch 140] average test loss: 2391.9748 cellbender:remove-background: [epoch 141] average training loss: 2359.7026 cellbender:remove-background: [epoch 142] average training loss: 2358.0250 cellbender:remove-background: [epoch 143] average training loss: 2355.1199 cellbender:remove-background: [epoch 144] average training loss: 2360.0718 cellbender:remove-background: [epoch 145] average training loss: 2358.9304 cellbender:remove-background: [epoch 145] average test loss: 2390.7772 cellbender:remove-background: [epoch 146] average training loss: 2357.3850 cellbender:remove-background: [epoch 147] average training loss: 2359.5999 cellbender:remove-background: [epoch 148] average training loss: 2362.0679 cellbender:remove-background: [epoch 149] average training loss: 2359.7060 cellbender:remove-background: [epoch 150] average training loss: 2354.5299 cellbender:remove-background: [epoch 150] average test loss: 2395.2424 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-dACC/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:34:37 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpnrigc8ac cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpnrigc8ac /tmp/tmpnrigc8ac/32fc3f2579_random.pyro /tmp/tmpnrigc8ac/32fc3f2579_random.cuda /tmp/tmpnrigc8ac/32fc3f2579_model.torch /tmp/tmpnrigc8ac/32fc3f2579_optim.torch /tmp/tmpnrigc8ac/32fc3f2579_optim.pyro /tmp/tmpnrigc8ac/32fc3f2579_params.pyro /tmp/tmpnrigc8ac/32fc3f2579_train.loaderstate /tmp/tmpnrigc8ac/32fc3f2579_test.loaderstate /tmp/tmpnrigc8ac/32fc3f2579_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 (1/46) cellbender:remove-background: [0.03 mins per chunk] cellbender:remove-background: Working on chunk (2/46) cellbender:remove-background: Working on chunk (3/46) cellbender:remove-background: Working on chunk (4/46) cellbender:remove-background: Working on chunk (5/46) cellbender:remove-background: Working on chunk (6/46) cellbender:remove-background: Working on chunk (7/46) cellbender:remove-background: Working on chunk (8/46) cellbender:remove-background: Working on chunk (9/46) cellbender:remove-background: Working on chunk (10/46) cellbender:remove-background: Working on chunk (11/46) cellbender:remove-background: Working on chunk (12/46) cellbender:remove-background: Working on chunk (13/46) cellbender:remove-background: Working on chunk (14/46) cellbender:remove-background: Working on chunk (15/46) cellbender:remove-background: Working on chunk (16/46) cellbender:remove-background: Working on chunk (17/46) cellbender:remove-background: Working on chunk (18/46) cellbender:remove-background: Working on chunk (19/46) cellbender:remove-background: Working on chunk (20/46) cellbender:remove-background: Working on chunk (21/46) cellbender:remove-background: Working on chunk (22/46) cellbender:remove-background: Working on chunk (23/46) cellbender:remove-background: Working on chunk (24/46) cellbender:remove-background: Working on chunk (25/46) cellbender:remove-background: Working on chunk (26/46) cellbender:remove-background: Working on chunk (27/46) cellbender:remove-background: Working on chunk (28/46) cellbender:remove-background: Working on chunk (29/46) cellbender:remove-background: Working on chunk (30/46) cellbender:remove-background: Working on chunk (31/46) cellbender:remove-background: Working on chunk (32/46) cellbender:remove-background: Working on chunk (33/46) cellbender:remove-background: Working on chunk (34/46) cellbender:remove-background: Working on chunk (35/46) cellbender:remove-background: Working on chunk (36/46) cellbender:remove-background: Working on chunk (37/46) cellbender:remove-background: Working on chunk (38/46) cellbender:remove-background: Working on chunk (39/46) cellbender:remove-background: Working on chunk (40/46) cellbender:remove-background: Working on chunk (41/46) cellbender:remove-background: Working on chunk (42/46) cellbender:remove-background: Working on chunk (43/46) cellbender:remove-background: Working on chunk (44/46) cellbender:remove-background: Working on chunk (45/46) cellbender:remove-background: Working on chunk (46/46) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1527-Schizophrenia-dACC/1527-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/1527-Schizophrenia-dACC/1527-Schizophrenia-dACC.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:38:12 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1527-Schizophrenia-dACC/1527-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/1527-Schizophrenia-dACC/1527-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: [1.66 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 15:50:12 Total MCKP estimation time = 694.16 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-dACC/1527-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/1527-Schizophrenia-dACC/1527-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/1527-Schizophrenia-dACC/1527-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/1527-Schizophrenia-dACC/1527-Schizophrenia-dACC.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:50:30