cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2677-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-Hippocampus/2677-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 13674 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash 949be3e4c0) cellbender:remove-background: 2024-06-06 14:48:29 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/2677-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: 30424 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 492 cellbender:remove-background: Prior on counts for empty droplets is 50 cellbender:remove-background: Excluding 7701 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 22723 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 25 cellbender:remove-background: Using 13674 probable cell barcodes, plus an additional 6326 barcodes, and 14965 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 49 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpcf9bn03a 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: 2684.8766 cellbender:remove-background: [epoch 002] average training loss: 2258.4720 (6.3 seconds per epoch) cellbender:remove-background: Will checkpoint every 67 epochs cellbender:remove-background: [epoch 003] average training loss: 2047.6354 cellbender:remove-background: [epoch 004] average training loss: 1913.3192 cellbender:remove-background: [epoch 005] average training loss: 1882.1207 cellbender:remove-background: [epoch 005] average test loss: 1898.9232 cellbender:remove-background: [epoch 006] average training loss: 1866.4949 cellbender:remove-background: [epoch 007] average training loss: 1851.3083 cellbender:remove-background: [epoch 008] average training loss: 1840.5633 cellbender:remove-background: [epoch 009] average training loss: 1835.0158 cellbender:remove-background: [epoch 010] average training loss: 1823.8577 cellbender:remove-background: [epoch 010] average test loss: 1855.8639 cellbender:remove-background: [epoch 011] average training loss: 1825.6222 cellbender:remove-background: [epoch 012] average training loss: 1809.3780 cellbender:remove-background: [epoch 013] average training loss: 1746.9959 cellbender:remove-background: [epoch 014] average training loss: 1731.5702 cellbender:remove-background: [epoch 015] average training loss: 1716.2395 cellbender:remove-background: [epoch 015] average test loss: 1743.4323 cellbender:remove-background: [epoch 016] average training loss: 1707.7894 cellbender:remove-background: [epoch 017] average training loss: 1702.7383 cellbender:remove-background: [epoch 018] average training loss: 1678.1447 cellbender:remove-background: [epoch 019] average training loss: 1658.8494 cellbender:remove-background: [epoch 020] average training loss: 1649.4486 cellbender:remove-background: [epoch 020] average test loss: 1676.4005 cellbender:remove-background: [epoch 021] average training loss: 1645.7962 cellbender:remove-background: [epoch 022] average training loss: 1643.4413 cellbender:remove-background: [epoch 023] average training loss: 1641.3255 cellbender:remove-background: [epoch 024] average training loss: 1635.7855 cellbender:remove-background: [epoch 025] average training loss: 1634.6567 cellbender:remove-background: [epoch 025] average test loss: 1653.1466 cellbender:remove-background: [epoch 026] average training loss: 1626.5991 cellbender:remove-background: [epoch 027] average training loss: 1625.5174 cellbender:remove-background: [epoch 028] average training loss: 1622.4511 cellbender:remove-background: [epoch 029] average training loss: 1617.8589 cellbender:remove-background: [epoch 030] average training loss: 1615.1256 cellbender:remove-background: [epoch 030] average test loss: 1634.8460 cellbender:remove-background: [epoch 031] average training loss: 1612.3553 cellbender:remove-background: [epoch 032] average training loss: 1609.4793 cellbender:remove-background: [epoch 033] average training loss: 1608.2288 cellbender:remove-background: [epoch 034] average training loss: 1606.6234 cellbender:remove-background: [epoch 035] average training loss: 1604.4900 cellbender:remove-background: [epoch 035] average test loss: 1622.2779 cellbender:remove-background: [epoch 036] average training loss: 1603.9677 cellbender:remove-background: [epoch 037] average training loss: 1600.9654 cellbender:remove-background: [epoch 038] average training loss: 1600.0265 cellbender:remove-background: [epoch 039] average training loss: 1600.1876 cellbender:remove-background: [epoch 040] average training loss: 1599.7547 cellbender:remove-background: [epoch 040] average test loss: 1619.0060 cellbender:remove-background: [epoch 041] average training loss: 1598.9046 cellbender:remove-background: [epoch 042] average training loss: 1597.6568 cellbender:remove-background: [epoch 043] average training loss: 1596.7213 cellbender:remove-background: [epoch 044] average training loss: 1595.0798 cellbender:remove-background: [epoch 045] average training loss: 1596.1754 cellbender:remove-background: [epoch 045] average test loss: 1613.7540 cellbender:remove-background: [epoch 046] average training loss: 1594.0319 cellbender:remove-background: [epoch 047] average training loss: 1593.0267 cellbender:remove-background: [epoch 048] average training loss: 1592.2171 cellbender:remove-background: [epoch 049] average training loss: 1593.0140 cellbender:remove-background: [epoch 050] average training loss: 1591.8078 cellbender:remove-background: [epoch 050] average test loss: 1610.0504 cellbender:remove-background: [epoch 051] average training loss: 1591.4183 cellbender:remove-background: [epoch 052] average training loss: 1589.6524 cellbender:remove-background: [epoch 053] average training loss: 1590.6985 cellbender:remove-background: [epoch 054] average training loss: 1589.3555 cellbender:remove-background: [epoch 055] average training loss: 1588.9249 cellbender:remove-background: [epoch 055] average test loss: 1612.4112 cellbender:remove-background: [epoch 056] average training loss: 1588.5459 cellbender:remove-background: [epoch 057] average training loss: 1588.7013 cellbender:remove-background: [epoch 058] average training loss: 1586.8584 cellbender:remove-background: [epoch 059] average training loss: 1586.6091 cellbender:remove-background: [epoch 060] average training loss: 1585.5905 cellbender:remove-background: [epoch 060] average test loss: 1606.2090 cellbender:remove-background: [epoch 061] average training loss: 1584.8152 cellbender:remove-background: [epoch 062] average training loss: 1585.3795 cellbender:remove-background: [epoch 063] average training loss: 1584.1336 cellbender:remove-background: [epoch 064] average training loss: 1583.8506 cellbender:remove-background: [epoch 065] average training loss: 1584.5391 cellbender:remove-background: [epoch 065] average test loss: 1604.6819 cellbender:remove-background: [epoch 066] average training loss: 1583.6829 cellbender:remove-background: [epoch 067] average training loss: 1583.2931 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/2677-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 068] average training loss: 1582.2589 cellbender:remove-background: [epoch 069] average training loss: 1581.4741 cellbender:remove-background: [epoch 070] average training loss: 1581.4671 cellbender:remove-background: [epoch 070] average test loss: 1605.4309 cellbender:remove-background: [epoch 071] average training loss: 1581.9826 cellbender:remove-background: [epoch 072] average training loss: 1580.7669 cellbender:remove-background: [epoch 073] average training loss: 1580.1523 cellbender:remove-background: [epoch 074] average training loss: 1579.2576 cellbender:remove-background: [epoch 075] average training loss: 1581.0871 cellbender:remove-background: [epoch 075] average test loss: 1600.2309 cellbender:remove-background: [epoch 076] average training loss: 1579.2174 cellbender:remove-background: [epoch 077] average training loss: 1578.6338 cellbender:remove-background: [epoch 078] average training loss: 1577.2323 cellbender:remove-background: [epoch 079] average training loss: 1578.9521 cellbender:remove-background: [epoch 080] average training loss: 1578.0548 cellbender:remove-background: [epoch 080] average test loss: 1597.1514 cellbender:remove-background: [epoch 081] average training loss: 1578.0848 cellbender:remove-background: [epoch 082] average training loss: 1577.5685 cellbender:remove-background: [epoch 083] average training loss: 1577.4294 cellbender:remove-background: [epoch 084] average training loss: 1576.2701 cellbender:remove-background: [epoch 085] average training loss: 1576.2165 cellbender:remove-background: [epoch 085] average test loss: 1605.7124 cellbender:remove-background: [epoch 086] average training loss: 1577.0632 cellbender:remove-background: [epoch 087] average training loss: 1575.9474 cellbender:remove-background: [epoch 088] average training loss: 1575.0620 cellbender:remove-background: [epoch 089] average training loss: 1574.6170 cellbender:remove-background: [epoch 090] average training loss: 1573.1757 cellbender:remove-background: [epoch 090] average test loss: 1596.7530 cellbender:remove-background: [epoch 091] average training loss: 1574.3860 cellbender:remove-background: [epoch 092] average training loss: 1572.7085 cellbender:remove-background: [epoch 093] average training loss: 1574.3916 cellbender:remove-background: [epoch 094] average training loss: 1572.4940 cellbender:remove-background: [epoch 095] average training loss: 1573.3721 cellbender:remove-background: [epoch 095] average test loss: 1605.0246 cellbender:remove-background: [epoch 096] average training loss: 1572.3226 cellbender:remove-background: [epoch 097] average training loss: 1571.8314 cellbender:remove-background: [epoch 098] average training loss: 1570.7327 cellbender:remove-background: [epoch 099] average training loss: 1571.3704 cellbender:remove-background: [epoch 100] average training loss: 1571.2858 cellbender:remove-background: [epoch 100] average test loss: 1601.4493 cellbender:remove-background: [epoch 101] average training loss: 1569.4687 cellbender:remove-background: [epoch 102] average training loss: 1571.1113 cellbender:remove-background: [epoch 103] average training loss: 1570.2449 cellbender:remove-background: [epoch 104] average training loss: 1570.2119 cellbender:remove-background: [epoch 105] average training loss: 1570.3531 cellbender:remove-background: [epoch 105] average test loss: 1599.8094 cellbender:remove-background: [epoch 106] average training loss: 1568.8699 cellbender:remove-background: [epoch 107] average training loss: 1569.1017 cellbender:remove-background: [epoch 108] average training loss: 1569.2034 cellbender:remove-background: [epoch 109] average training loss: 1568.6986 cellbender:remove-background: [epoch 110] average training loss: 1567.9687 cellbender:remove-background: [epoch 110] average test loss: 1595.2634 cellbender:remove-background: [epoch 111] average training loss: 1568.7807 cellbender:remove-background: [epoch 112] average training loss: 1568.2012 cellbender:remove-background: [epoch 113] average training loss: 1568.0957 cellbender:remove-background: [epoch 114] average training loss: 1566.5642 cellbender:remove-background: [epoch 115] average training loss: 1567.0109 cellbender:remove-background: [epoch 115] average test loss: 1603.3325 cellbender:remove-background: [epoch 116] average training loss: 1566.2260 cellbender:remove-background: [epoch 117] average training loss: 1565.4564 cellbender:remove-background: [epoch 118] average training loss: 1565.5045 cellbender:remove-background: [epoch 119] average training loss: 1565.8079 cellbender:remove-background: [epoch 120] average training loss: 1565.6440 cellbender:remove-background: [epoch 120] average test loss: 1596.9117 cellbender:remove-background: [epoch 121] average training loss: 1566.1047 cellbender:remove-background: [epoch 122] average training loss: 1565.5121 cellbender:remove-background: [epoch 123] average training loss: 1565.7076 cellbender:remove-background: [epoch 124] average training loss: 1565.5570 cellbender:remove-background: [epoch 125] average training loss: 1565.6618 cellbender:remove-background: [epoch 125] average test loss: 1598.1699 cellbender:remove-background: [epoch 126] average training loss: 1565.3105 cellbender:remove-background: [epoch 127] average training loss: 1565.1743 cellbender:remove-background: [epoch 128] average training loss: 1565.1528 cellbender:remove-background: [epoch 129] average training loss: 1565.8873 cellbender:remove-background: [epoch 130] average training loss: 1563.7871 cellbender:remove-background: [epoch 130] average test loss: 1600.5286 cellbender:remove-background: [epoch 131] average training loss: 1565.8223 cellbender:remove-background: [epoch 132] average training loss: 1564.1997 cellbender:remove-background: [epoch 133] average training loss: 1564.6930 cellbender:remove-background: [epoch 134] average training loss: 1564.0618 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/2677-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: [epoch 135] average training loss: 1564.9267 cellbender:remove-background: [epoch 135] average test loss: 1596.6789 cellbender:remove-background: [epoch 136] average training loss: 1563.8576 cellbender:remove-background: [epoch 137] average training loss: 1563.7688 cellbender:remove-background: [epoch 138] average training loss: 1565.1476 cellbender:remove-background: [epoch 139] average training loss: 1563.6335 cellbender:remove-background: [epoch 140] average training loss: 1563.1992 cellbender:remove-background: [epoch 140] average test loss: 1598.2773 cellbender:remove-background: [epoch 141] average training loss: 1564.0059 cellbender:remove-background: [epoch 142] average training loss: 1564.3236 cellbender:remove-background: [epoch 143] average training loss: 1563.5611 cellbender:remove-background: [epoch 144] average training loss: 1563.7002 cellbender:remove-background: [epoch 145] average training loss: 1564.2345 cellbender:remove-background: [epoch 145] average test loss: 1598.3793 cellbender:remove-background: [epoch 146] average training loss: 1563.8224 cellbender:remove-background: [epoch 147] average training loss: 1562.9797 cellbender:remove-background: [epoch 148] average training loss: 1563.9996 cellbender:remove-background: [epoch 149] average training loss: 1563.5202 cellbender:remove-background: [epoch 150] average training loss: 1564.9138 cellbender:remove-background: [epoch 150] average test loss: 1597.5320 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/2677-Schizophrenia-Hippocampus/ckpt.tar.gz cellbender:remove-background: 2024-06-06 15:06:33 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpa75crwmk cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpa75crwmk /tmp/tmpa75crwmk/949be3e4c0_random.pyro /tmp/tmpa75crwmk/949be3e4c0_random.cuda /tmp/tmpa75crwmk/949be3e4c0_model.torch /tmp/tmpa75crwmk/949be3e4c0_optim.torch /tmp/tmpa75crwmk/949be3e4c0_optim.pyro /tmp/tmpa75crwmk/949be3e4c0_params.pyro /tmp/tmpa75crwmk/949be3e4c0_train.loaderstate /tmp/tmpa75crwmk/949be3e4c0_test.loaderstate /tmp/tmpa75crwmk/949be3e4c0_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 (1/92) cellbender:remove-background: [0.04 mins per chunk] cellbender:remove-background: Working on chunk (2/92) cellbender:remove-background: Working on chunk (3/92) cellbender:remove-background: Working on chunk (4/92) cellbender:remove-background: Working on chunk (5/92) cellbender:remove-background: Working on chunk (6/92) cellbender:remove-background: Working on chunk (7/92) cellbender:remove-background: Working on chunk (8/92) cellbender:remove-background: Working on chunk (9/92) cellbender:remove-background: Working on chunk (10/92) cellbender:remove-background: Working on chunk (11/92) cellbender:remove-background: Working on chunk (12/92) cellbender:remove-background: Working on chunk (13/92) cellbender:remove-background: Working on chunk (14/92) cellbender:remove-background: Working on chunk (15/92) cellbender:remove-background: Working on chunk (16/92) cellbender:remove-background: Working on chunk (17/92) cellbender:remove-background: Working on chunk (18/92) cellbender:remove-background: Working on chunk (19/92) cellbender:remove-background: Working on chunk (20/92) cellbender:remove-background: Working on chunk (21/92) cellbender:remove-background: Working on chunk (22/92) cellbender:remove-background: Working on chunk (23/92) cellbender:remove-background: Working on chunk (24/92) cellbender:remove-background: Working on chunk (25/92) cellbender:remove-background: Working on chunk (26/92) cellbender:remove-background: Working on chunk (27/92) cellbender:remove-background: Working on chunk (28/92) cellbender:remove-background: Working on chunk (29/92) cellbender:remove-background: Working on chunk (30/92) cellbender:remove-background: Working on chunk (31/92) cellbender:remove-background: Working on chunk (32/92) cellbender:remove-background: Working on chunk (33/92) cellbender:remove-background: Working on chunk (34/92) cellbender:remove-background: Working on chunk (35/92) cellbender:remove-background: Working on chunk (36/92) cellbender:remove-background: Working on chunk (37/92) cellbender:remove-background: Working on chunk (38/92) cellbender:remove-background: Working on chunk (39/92) cellbender:remove-background: Working on chunk (40/92) cellbender:remove-background: Working on chunk (41/92) cellbender:remove-background: Working on chunk (42/92) cellbender:remove-background: Working on chunk (43/92) cellbender:remove-background: Working on chunk (44/92) cellbender:remove-background: Working on chunk (45/92) cellbender:remove-background: Working on chunk (46/92) cellbender:remove-background: Working on chunk (47/92) cellbender:remove-background: Working on chunk (48/92) cellbender:remove-background: Working on chunk (49/92) cellbender:remove-background: Working on chunk (50/92) cellbender:remove-background: Working on chunk (51/92) cellbender:remove-background: Working on chunk (52/92) cellbender:remove-background: Working on chunk (53/92) cellbender:remove-background: Working on chunk (54/92) cellbender:remove-background: Working on chunk (55/92) cellbender:remove-background: Working on chunk (56/92) cellbender:remove-background: Working on chunk (57/92) cellbender:remove-background: Working on chunk (58/92) cellbender:remove-background: Working on chunk (59/92) cellbender:remove-background: Working on chunk (60/92) cellbender:remove-background: Working on chunk (61/92) cellbender:remove-background: Working on chunk (62/92) cellbender:remove-background: Working on chunk (63/92) cellbender:remove-background: Working on chunk (64/92) cellbender:remove-background: Working on chunk (65/92) cellbender:remove-background: Working on chunk (66/92) cellbender:remove-background: Working on chunk (67/92) cellbender:remove-background: Working on chunk (68/92) cellbender:remove-background: Working on chunk (69/92) cellbender:remove-background: Working on chunk (70/92) cellbender:remove-background: Working on chunk (71/92) cellbender:remove-background: Working on chunk (72/92) cellbender:remove-background: Working on chunk (73/92) cellbender:remove-background: Working on chunk (74/92) cellbender:remove-background: Working on chunk (75/92) cellbender:remove-background: Working on chunk (76/92) cellbender:remove-background: Working on chunk (77/92) cellbender:remove-background: Working on chunk (78/92) cellbender:remove-background: Working on chunk (79/92) cellbender:remove-background: Working on chunk (80/92) cellbender:remove-background: Working on chunk (81/92) cellbender:remove-background: Working on chunk (82/92) cellbender:remove-background: Working on chunk (83/92) cellbender:remove-background: Working on chunk (84/92) cellbender:remove-background: Working on chunk (85/92) cellbender:remove-background: Working on chunk (86/92) cellbender:remove-background: Working on chunk (87/92) cellbender:remove-background: Working on chunk (88/92) cellbender:remove-background: Working on chunk (89/92) cellbender:remove-background: Working on chunk (90/92) cellbender:remove-background: Working on chunk (91/92) cellbender:remove-background: Working on chunk (92/92) cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-Hippocampus/2677-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/2677-Schizophrenia-Hippocampus/2677-Schizophrenia-Hippocampus.cellbender.output_posterior.h5 cellbender:remove-background: Added posterior object to checkpoint file. cellbender:remove-background: 2024-06-06 15:11:24 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2677-Schizophrenia-Hippocampus/2677-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/2677-Schizophrenia-Hippocampus/2677-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: [0.73 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 15:16:46 Total MCKP estimation time = 307.86 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/2677-Schizophrenia-Hippocampus/2677-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/2677-Schizophrenia-Hippocampus/2677-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/2677-Schizophrenia-Hippocampus/2677-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/2677-Schizophrenia-Hippocampus/2677-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 15:16:59