cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1320-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-Hippocampus/1320-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 9404 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 5a8eb93de9) cellbender:remove-background: 2024-06-06 15:38:07 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/1320-Schizophrenia-Hippocampus.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: 30960 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 1226 cellbender:remove-background: Prior on counts for empty droplets is 34 cellbender:remove-background: Excluding 9344 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21616 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 17 cellbender:remove-background: Using 9404 probable cell barcodes, plus an additional 10596 barcodes, and 32387 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 33 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpq342r46l 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: 3506.0266 cellbender:remove-background: [epoch 002] average training loss: 2835.4348 (6.2 seconds per epoch) cellbender:remove-background: Will checkpoint every 68 epochs cellbender:remove-background: [epoch 003] average training loss: 2474.6971 cellbender:remove-background: [epoch 004] average training loss: 2234.6971 cellbender:remove-background: [epoch 005] average training loss: 2174.1592 cellbender:remove-background: [epoch 005] average test loss: 2291.1802 cellbender:remove-background: [epoch 006] average training loss: 2160.3823 cellbender:remove-background: [epoch 007] average training loss: 2120.6755 cellbender:remove-background: [epoch 008] average training loss: 2105.1096 cellbender:remove-background: [epoch 009] average training loss: 2104.7045 cellbender:remove-background: [epoch 010] average training loss: 2073.2888 cellbender:remove-background: [epoch 010] average test loss: 2108.7686 cellbender:remove-background: [epoch 011] average training loss: 2028.6835 cellbender:remove-background: [epoch 012] average training loss: 1936.0071 cellbender:remove-background: [epoch 013] average training loss: 1911.5523 cellbender:remove-background: [epoch 014] average training loss: 1905.8559 cellbender:remove-background: [epoch 015] average training loss: 1883.5938 cellbender:remove-background: [epoch 015] average test loss: 1938.2470 cellbender:remove-background: [epoch 016] average training loss: 1879.6940 cellbender:remove-background: [epoch 017] average training loss: 1876.8621 cellbender:remove-background: [epoch 018] average training loss: 1865.7863 cellbender:remove-background: [epoch 019] average training loss: 1855.1641 cellbender:remove-background: [epoch 020] average training loss: 1847.0786 cellbender:remove-background: [epoch 020] average test loss: 1912.6973 cellbender:remove-background: [epoch 021] average training loss: 1845.5884 cellbender:remove-background: [epoch 022] average training loss: 1845.1739 cellbender:remove-background: [epoch 023] average training loss: 1839.6203 cellbender:remove-background: [epoch 024] average training loss: 1835.5298 cellbender:remove-background: [epoch 025] average training loss: 1834.7278 cellbender:remove-background: [epoch 025] average test loss: 1870.4066 cellbender:remove-background: [epoch 026] average training loss: 1826.5060 cellbender:remove-background: [epoch 027] average training loss: 1820.9032 cellbender:remove-background: [epoch 028] average training loss: 1813.2738 cellbender:remove-background: [epoch 029] average training loss: 1803.9437 cellbender:remove-background: [epoch 030] average training loss: 1794.5471 cellbender:remove-background: [epoch 030] average test loss: 1843.8900 cellbender:remove-background: [epoch 031] average training loss: 1790.3351 cellbender:remove-background: [epoch 032] average training loss: 1785.8183 cellbender:remove-background: [epoch 033] average training loss: 1782.9786 cellbender:remove-background: [epoch 034] average training loss: 1780.4112 cellbender:remove-background: [epoch 035] average training loss: 1773.8308 cellbender:remove-background: [epoch 035] average test loss: 1817.8679 cellbender:remove-background: [epoch 036] average training loss: 1774.8123 cellbender:remove-background: [epoch 037] average training loss: 1771.8946 cellbender:remove-background: [epoch 038] average training loss: 1768.3651 cellbender:remove-background: [epoch 039] average training loss: 1770.5619 cellbender:remove-background: [epoch 040] average training loss: 1769.3327 cellbender:remove-background: [epoch 040] average test loss: 1804.4808 cellbender:remove-background: [epoch 041] average training loss: 1770.5422 cellbender:remove-background: [epoch 042] average training loss: 1768.7188 cellbender:remove-background: [epoch 043] average training loss: 1766.0104 cellbender:remove-background: [epoch 044] average training loss: 1765.4179 cellbender:remove-background: [epoch 045] average training loss: 1766.1562 cellbender:remove-background: [epoch 045] average test loss: 1792.1303 cellbender:remove-background: [epoch 046] average training loss: 1765.6228 cellbender:remove-background: [epoch 047] average training loss: 1763.5071 cellbender:remove-background: [epoch 048] average training loss: 1763.7941 cellbender:remove-background: [epoch 049] average training loss: 1761.3213 cellbender:remove-background: [epoch 050] average training loss: 1760.9471 cellbender:remove-background: [epoch 050] average test loss: 1808.2611 cellbender:remove-background: [epoch 051] average training loss: 1759.6210 cellbender:remove-background: [epoch 052] average training loss: 1758.2437 cellbender:remove-background: [epoch 053] average training loss: 1756.7442 cellbender:remove-background: [epoch 054] average training loss: 1757.2787 cellbender:remove-background: [epoch 055] average training loss: 1757.2618 cellbender:remove-background: [epoch 055] average test loss: 1806.8874 cellbender:remove-background: [epoch 056] average training loss: 1756.3369 cellbender:remove-background: [epoch 057] average training loss: 1755.2979 cellbender:remove-background: [epoch 058] average training loss: 1751.8052 cellbender:remove-background: [epoch 059] average training loss: 1752.2990 cellbender:remove-background: [epoch 060] average training loss: 1750.9678 cellbender:remove-background: [epoch 060] average test loss: 1795.6333 cellbender:remove-background: [epoch 061] average training loss: 1750.7003 cellbender:remove-background: [epoch 062] average training loss: 1753.0132 cellbender:remove-background: [epoch 063] average training loss: 1747.6175 cellbender:remove-background: [epoch 064] average training loss: 1748.0697 cellbender:remove-background: [epoch 065] average training loss: 1748.1767 cellbender:remove-background: [epoch 065] average test loss: 1787.6476 cellbender:remove-background: [epoch 066] average training loss: 1748.8000 cellbender:remove-background: [epoch 067] average training loss: 1746.4050 cellbender:remove-background: [epoch 068] average training loss: 1745.7555 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/1320-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 069] average training loss: 1743.1229 cellbender:remove-background: [epoch 070] average training loss: 1742.0787 cellbender:remove-background: [epoch 070] average test loss: 1788.1990 cellbender:remove-background: [epoch 071] average training loss: 1740.7961 cellbender:remove-background: [epoch 072] average training loss: 1742.7340 cellbender:remove-background: [epoch 073] average training loss: 1741.7563 cellbender:remove-background: [epoch 074] average training loss: 1740.0788 cellbender:remove-background: [epoch 075] average training loss: 1741.1724 cellbender:remove-background: [epoch 075] average test loss: 1780.4545 cellbender:remove-background: [epoch 076] average training loss: 1736.4257 cellbender:remove-background: [epoch 077] average training loss: 1739.6782 cellbender:remove-background: [epoch 078] average training loss: 1738.0520 cellbender:remove-background: [epoch 079] average training loss: 1733.4922 cellbender:remove-background: [epoch 080] average training loss: 1733.6024 cellbender:remove-background: [epoch 080] average test loss: 1783.7403 cellbender:remove-background: [epoch 081] average training loss: 1735.2538 cellbender:remove-background: [epoch 082] average training loss: 1735.8853 cellbender:remove-background: [epoch 083] average training loss: 1731.7233 cellbender:remove-background: [epoch 084] average training loss: 1731.7262 cellbender:remove-background: [epoch 085] average training loss: 1733.6531 cellbender:remove-background: [epoch 085] average test loss: 1771.5521 cellbender:remove-background: [epoch 086] average training loss: 1730.7682 cellbender:remove-background: [epoch 087] average training loss: 1729.9005 cellbender:remove-background: [epoch 088] average training loss: 1728.9660 cellbender:remove-background: [epoch 089] average training loss: 1727.7250 cellbender:remove-background: [epoch 090] average training loss: 1729.9149 cellbender:remove-background: [epoch 090] average test loss: 1780.7375 cellbender:remove-background: [epoch 091] average training loss: 1729.9321 cellbender:remove-background: [epoch 092] average training loss: 1727.4133 cellbender:remove-background: [epoch 093] average training loss: 1727.2101 cellbender:remove-background: [epoch 094] average training loss: 1727.4265 cellbender:remove-background: [epoch 095] average training loss: 1727.3802 cellbender:remove-background: [epoch 095] average test loss: 1776.1211 cellbender:remove-background: [epoch 096] average training loss: 1727.9147 cellbender:remove-background: [epoch 097] average training loss: 1726.1865 cellbender:remove-background: [epoch 098] average training loss: 1725.9861 cellbender:remove-background: [epoch 099] average training loss: 1725.5365 cellbender:remove-background: [epoch 100] average training loss: 1724.9904 cellbender:remove-background: [epoch 100] average test loss: 1775.2192 cellbender:remove-background: [epoch 101] average training loss: 1725.0926 cellbender:remove-background: [epoch 102] average training loss: 1724.6609 cellbender:remove-background: [epoch 103] average training loss: 1722.1854 cellbender:remove-background: [epoch 104] average training loss: 1723.5239 cellbender:remove-background: [epoch 105] average training loss: 1723.1491 cellbender:remove-background: [epoch 105] average test loss: 1769.6613 cellbender:remove-background: [epoch 106] average training loss: 1721.7764 cellbender:remove-background: [epoch 107] average training loss: 1723.0312 cellbender:remove-background: [epoch 108] average training loss: 1722.0472 cellbender:remove-background: [epoch 109] average training loss: 1721.2991 cellbender:remove-background: [epoch 110] average training loss: 1722.3407 cellbender:remove-background: [epoch 110] average test loss: 1769.1882 cellbender:remove-background: [epoch 111] average training loss: 1721.2427 cellbender:remove-background: [epoch 112] average training loss: 1721.9837 cellbender:remove-background: [epoch 113] average training loss: 1720.4468 cellbender:remove-background: [epoch 114] average training loss: 1720.3881 cellbender:remove-background: [epoch 115] average training loss: 1719.3055 cellbender:remove-background: [epoch 115] average test loss: 1773.0869 cellbender:remove-background: [epoch 116] average training loss: 1719.7828 cellbender:remove-background: [epoch 117] average training loss: 1720.0382 cellbender:remove-background: [epoch 118] average training loss: 1719.5360 cellbender:remove-background: [epoch 119] average training loss: 1719.8931 cellbender:remove-background: [epoch 120] average training loss: 1718.9673 cellbender:remove-background: [epoch 120] average test loss: 1769.4343 cellbender:remove-background: [epoch 121] average training loss: 1719.3485 cellbender:remove-background: [epoch 122] average training loss: 1719.1932 cellbender:remove-background: [epoch 123] average training loss: 1718.1814 cellbender:remove-background: [epoch 124] average training loss: 1717.6982 cellbender:remove-background: [epoch 125] average training loss: 1718.0567 cellbender:remove-background: [epoch 125] average test loss: 1772.5490 cellbender:remove-background: [epoch 126] average training loss: 1717.3294 cellbender:remove-background: [epoch 127] average training loss: 1718.3355 cellbender:remove-background: [epoch 128] average training loss: 1718.4526 cellbender:remove-background: [epoch 129] average training loss: 1717.7168 cellbender:remove-background: [epoch 130] average training loss: 1716.9196 cellbender:remove-background: [epoch 130] average test loss: 1770.0048 cellbender:remove-background: [epoch 131] average training loss: 1716.1794 cellbender:remove-background: [epoch 132] average training loss: 1718.2610 cellbender:remove-background: [epoch 133] average training loss: 1716.9569 cellbender:remove-background: [epoch 134] average training loss: 1715.6775 cellbender:remove-background: [epoch 135] average training loss: 1715.2837 cellbender:remove-background: [epoch 135] average test loss: 1769.3353 cellbender:remove-background: [epoch 136] average training loss: 1716.7014 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/1320-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 137] average training loss: 1715.8618 cellbender:remove-background: [epoch 138] average training loss: 1715.0566 cellbender:remove-background: [epoch 139] average training loss: 1716.0108 cellbender:remove-background: [epoch 140] average training loss: 1715.4471 cellbender:remove-background: [epoch 140] average test loss: 1770.7683 cellbender:remove-background: [epoch 141] average training loss: 1716.9897 cellbender:remove-background: [epoch 142] average training loss: 1716.2511 cellbender:remove-background: [epoch 143] average training loss: 1715.4517 cellbender:remove-background: [epoch 144] average training loss: 1715.5318 cellbender:remove-background: [epoch 145] average training loss: 1715.5604 cellbender:remove-background: [epoch 145] average test loss: 1771.7119 cellbender:remove-background: [epoch 146] average training loss: 1715.5590 cellbender:remove-background: [epoch 147] average training loss: 1715.6080 cellbender:remove-background: [epoch 148] average training loss: 1715.0757 cellbender:remove-background: [epoch 149] average training loss: 1714.7424 cellbender:remove-background: [epoch 150] average training loss: 1714.1025 cellbender:remove-background: [epoch 150] average test loss: 1768.5964 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/1320-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:57:30 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpd3tuwo8k cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpd3tuwo8k /tmp/tmpd3tuwo8k/5a8eb93de9_random.pyro /tmp/tmpd3tuwo8k/5a8eb93de9_random.cuda /tmp/tmpd3tuwo8k/5a8eb93de9_model.torch /tmp/tmpd3tuwo8k/5a8eb93de9_optim.torch /tmp/tmpd3tuwo8k/5a8eb93de9_optim.pyro /tmp/tmpd3tuwo8k/5a8eb93de9_params.pyro /tmp/tmpd3tuwo8k/5a8eb93de9_train.loaderstate /tmp/tmpd3tuwo8k/5a8eb93de9_test.loaderstate /tmp/tmpd3tuwo8k/5a8eb93de9_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 (1/74) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/74) cellbender:remove-background: Working on chunk (3/74) cellbender:remove-background: Working on chunk (4/74) cellbender:remove-background: Working on chunk (5/74) cellbender:remove-background: Working on chunk (6/74) cellbender:remove-background: Working on chunk (7/74) cellbender:remove-background: Working on chunk (8/74) cellbender:remove-background: Working on chunk (9/74) cellbender:remove-background: Working on chunk (10/74) cellbender:remove-background: Working on chunk (11/74) cellbender:remove-background: Working on chunk (12/74) cellbender:remove-background: Working on chunk (13/74) cellbender:remove-background: Working on chunk (14/74) cellbender:remove-background: Working on chunk (15/74) cellbender:remove-background: Working on chunk (16/74) cellbender:remove-background: Working on chunk (17/74) cellbender:remove-background: Working on chunk (18/74) cellbender:remove-background: Working on chunk (19/74) cellbender:remove-background: Working on chunk (20/74) cellbender:remove-background: Working on chunk (21/74) cellbender:remove-background: Working on chunk (22/74) cellbender:remove-background: Working on chunk (23/74) cellbender:remove-background: Working on chunk (24/74) cellbender:remove-background: Working on chunk (25/74) cellbender:remove-background: Working on chunk (26/74) cellbender:remove-background: Working on chunk (27/74) cellbender:remove-background: Working on chunk (28/74) cellbender:remove-background: Working on chunk (29/74) cellbender:remove-background: Working on chunk (30/74) cellbender:remove-background: Working on chunk (31/74) cellbender:remove-background: Working on chunk (32/74) cellbender:remove-background: Working on chunk (33/74) cellbender:remove-background: Working on chunk (34/74) cellbender:remove-background: Working on chunk (35/74) cellbender:remove-background: Working on chunk (36/74) cellbender:remove-background: Working on chunk (37/74) cellbender:remove-background: Working on chunk (38/74) cellbender:remove-background: Working on chunk (39/74) cellbender:remove-background: Working on chunk (40/74) cellbender:remove-background: Working on chunk (41/74) cellbender:remove-background: Working on chunk (42/74) cellbender:remove-background: Working on chunk (43/74) cellbender:remove-background: Working on chunk (44/74) cellbender:remove-background: Working on chunk (45/74) cellbender:remove-background: Working on chunk (46/74) cellbender:remove-background: Working on chunk (47/74) cellbender:remove-background: Working on chunk (48/74) cellbender:remove-background: Working on chunk (49/74) cellbender:remove-background: Working on chunk (50/74) cellbender:remove-background: Working on chunk (51/74) cellbender:remove-background: Working on chunk (52/74) cellbender:remove-background: Working on chunk (53/74) cellbender:remove-background: Working on chunk (54/74) cellbender:remove-background: Working on chunk (55/74) cellbender:remove-background: Working on chunk (56/74) cellbender:remove-background: Working on chunk (57/74) cellbender:remove-background: Working on chunk (58/74) cellbender:remove-background: Working on chunk (59/74) cellbender:remove-background: Working on chunk (60/74) cellbender:remove-background: Working on chunk (61/74) cellbender:remove-background: Working on chunk (62/74) cellbender:remove-background: Working on chunk (63/74) cellbender:remove-background: Working on chunk (64/74) cellbender:remove-background: Working on chunk (65/74) cellbender:remove-background: Working on chunk (66/74) cellbender:remove-background: Working on chunk (67/74) cellbender:remove-background: Working on chunk (68/74) cellbender:remove-background: Working on chunk (69/74) cellbender:remove-background: Working on chunk (70/74) cellbender:remove-background: Working on chunk (71/74) cellbender:remove-background: Working on chunk (72/74) cellbender:remove-background: Working on chunk (73/74) cellbender:remove-background: Working on chunk (74/74) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-Hippocampus/1320-Schizophrenia-Hippocampus.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/1320-Schizophrenia-Hippocampus/1320-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 16:01:36 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-Hippocampus/1320-Schizophrenia-Hippocampus.cellbender.output.pdf cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-Hippocampus/1320-Schizophrenia-Hippocampus.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: [1.06 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 16:09:21 Total MCKP estimation time = 446.39 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/1320-Schizophrenia-Hippocampus/1320-Schizophrenia-Hippocampus.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/1320-Schizophrenia-Hippocampus/1320-Schizophrenia-Hippocampus.cellbender.output_filtered.h5 cellbender:remove-background: Saved output metrics as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1320-Schizophrenia-Hippocampus/1320-Schizophrenia-Hippocampus.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/1320-Schizophrenia-Hippocampus/1320-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:09:35