cellbender:remove-background: Command:
cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/2083-Bipolar-DLPFC.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-DLPFC/2083-Bipolar-DLPFC.cellbender.output.h5 --cuda --expected-cells 11955 --total-droplets-included 20000 --fpr 0.01 --epochs 150
cellbender:remove-background: CellBender 0.3.0
cellbender:remove-background: (Workflow hash 4dbed8f123)
cellbender:remove-background: 2024-06-06 14:54:30
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/2083-Bipolar-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: 32570 features have nonzero counts.
cellbender:remove-background: Prior on counts for cells is 3792
cellbender:remove-background: Prior on counts for empty droplets is 141
cellbender:remove-background: Excluding 7491 features that are estimated to have <= 0.1 background counts in cells.
cellbender:remove-background: Including 25079 features in the analysis.
cellbender:remove-background: Trimming barcodes for inference.
cellbender:remove-background: Excluding barcodes with counts below 70
cellbender:remove-background: Using 11955 probable cell barcodes, plus an additional 8045 barcodes, and 20036 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 139 UMI counts.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpsyaovg88
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: 9878.1496
cellbender:remove-background: [epoch 002]  average training loss: 7374.2438  (7.0 seconds per epoch)
cellbender:remove-background: Will checkpoint every 60 epochs
cellbender:remove-background: [epoch 003]  average training loss: 6027.6302
cellbender:remove-background: [epoch 004]  average training loss: 5241.9056
cellbender:remove-background: [epoch 005]  average training loss: 4972.8152
cellbender:remove-background: [epoch 005] average test loss: 5009.1381
cellbender:remove-background: [epoch 006]  average training loss: 4878.6040
cellbender:remove-background: [epoch 007]  average training loss: 4808.5377
cellbender:remove-background: [epoch 008]  average training loss: 4764.7099
cellbender:remove-background: [epoch 009]  average training loss: 4747.1726
cellbender:remove-background: [epoch 010]  average training loss: 4670.8358
cellbender:remove-background: [epoch 010] average test loss: 4705.0983
cellbender:remove-background: [epoch 011]  average training loss: 4603.3996
cellbender:remove-background: [epoch 012]  average training loss: 4566.0165
cellbender:remove-background: [epoch 013]  average training loss: 4537.0700
cellbender:remove-background: [epoch 014]  average training loss: 4544.5758
cellbender:remove-background: [epoch 015]  average training loss: 4511.8291
cellbender:remove-background: [epoch 015] average test loss: 4545.3546
cellbender:remove-background: [epoch 016]  average training loss: 4494.4402
cellbender:remove-background: [epoch 017]  average training loss: 4502.9529
cellbender:remove-background: [epoch 018]  average training loss: 4483.5945
cellbender:remove-background: [epoch 019]  average training loss: 4465.8827
cellbender:remove-background: [epoch 020]  average training loss: 4438.3072
cellbender:remove-background: [epoch 020] average test loss: 4425.2279
cellbender:remove-background: [epoch 021]  average training loss: 4431.0153
cellbender:remove-background: [epoch 022]  average training loss: 4422.3497
cellbender:remove-background: [epoch 023]  average training loss: 4409.2270
cellbender:remove-background: [epoch 024]  average training loss: 4385.8043
cellbender:remove-background: [epoch 025]  average training loss: 4373.4404
cellbender:remove-background: [epoch 025] average test loss: 4323.1790
cellbender:remove-background: [epoch 026]  average training loss: 4351.3002
cellbender:remove-background: [epoch 027]  average training loss: 4345.8424
cellbender:remove-background: [epoch 028]  average training loss: 4339.2757
cellbender:remove-background: [epoch 029]  average training loss: 4326.4314
cellbender:remove-background: [epoch 030]  average training loss: 4323.5372
cellbender:remove-background: [epoch 030] average test loss: 4263.9864
cellbender:remove-background: [epoch 031]  average training loss: 4321.1040
cellbender:remove-background: [epoch 032]  average training loss: 4316.4849
cellbender:remove-background: [epoch 033]  average training loss: 4314.9618
cellbender:remove-background: [epoch 034]  average training loss: 4309.7960
cellbender:remove-background: [epoch 035]  average training loss: 4307.2898
cellbender:remove-background: [epoch 035] average test loss: 4265.1283
cellbender:remove-background: [epoch 036]  average training loss: 4307.8109
cellbender:remove-background: [epoch 037]  average training loss: 4308.8733
cellbender:remove-background: [epoch 038]  average training loss: 4302.7262
cellbender:remove-background: [epoch 039]  average training loss: 4305.4539
cellbender:remove-background: [epoch 040]  average training loss: 4300.3694
cellbender:remove-background: [epoch 040] average test loss: 4232.7489
cellbender:remove-background: [epoch 041]  average training loss: 4300.3735
cellbender:remove-background: [epoch 042]  average training loss: 4298.9084
cellbender:remove-background: [epoch 043]  average training loss: 4296.2685
cellbender:remove-background: [epoch 044]  average training loss: 4294.8017
cellbender:remove-background: [epoch 045]  average training loss: 4293.7093
cellbender:remove-background: [epoch 045] average test loss: 4229.7854
cellbender:remove-background: [epoch 046]  average training loss: 4295.6250
cellbender:remove-background: [epoch 047]  average training loss: 4292.1839
cellbender:remove-background: [epoch 048]  average training loss: 4292.3621
cellbender:remove-background: [epoch 049]  average training loss: 4288.4235
cellbender:remove-background: [epoch 050]  average training loss: 4286.5892
cellbender:remove-background: [epoch 050] average test loss: 4228.5541
cellbender:remove-background: [epoch 051]  average training loss: 4286.1836
cellbender:remove-background: [epoch 052]  average training loss: 4280.1094
cellbender:remove-background: [epoch 053]  average training loss: 4276.8145
cellbender:remove-background: [epoch 054]  average training loss: 4281.7043
cellbender:remove-background: [epoch 055]  average training loss: 4275.6100
cellbender:remove-background: [epoch 055] average test loss: 4205.9824
cellbender:remove-background: [epoch 056]  average training loss: 4275.4938
cellbender:remove-background: [epoch 057]  average training loss: 4278.8780
cellbender:remove-background: [epoch 058]  average training loss: 4269.9526
cellbender:remove-background: [epoch 059]  average training loss: 4272.3898
cellbender:remove-background: [epoch 060]  average training loss: 4270.4347
cellbender:remove-background: [epoch 060] average test loss: 4237.0147
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/2083-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 061]  average training loss: 4268.1233
cellbender:remove-background: [epoch 062]  average training loss: 4277.4842
cellbender:remove-background: [epoch 063]  average training loss: 4287.1175
cellbender:remove-background: [epoch 064]  average training loss: 4283.4084
cellbender:remove-background: [epoch 065]  average training loss: 4277.1101
cellbender:remove-background: [epoch 065] average test loss: 4217.8578
cellbender:remove-background: [epoch 066]  average training loss: 4271.2960
cellbender:remove-background: [epoch 067]  average training loss: 4264.6142
cellbender:remove-background: [epoch 068]  average training loss: 4271.1658
cellbender:remove-background: [epoch 069]  average training loss: 4262.2639
cellbender:remove-background: [epoch 070]  average training loss: 4266.0091
cellbender:remove-background: [epoch 070] average test loss: 4244.7197
cellbender:remove-background: [epoch 071]  average training loss: 4268.6258
cellbender:remove-background: [epoch 072]  average training loss: 4272.1785
cellbender:remove-background: [epoch 073]  average training loss: 4274.2102
cellbender:remove-background: [epoch 074]  average training loss: 4271.1607
cellbender:remove-background: [epoch 075]  average training loss: 4274.3234
cellbender:remove-background: [epoch 075] average test loss: 4247.8654
cellbender:remove-background: [epoch 076]  average training loss: 4272.1051
cellbender:remove-background: [epoch 077]  average training loss: 4266.2328
cellbender:remove-background: [epoch 078]  average training loss: 4270.3033
cellbender:remove-background: [epoch 079]  average training loss: 4273.9885
cellbender:remove-background: [epoch 080]  average training loss: 4265.8867
cellbender:remove-background: [epoch 080] average test loss: 4267.6267
cellbender:remove-background: [epoch 081]  average training loss: 4293.5791
cellbender:remove-background: [epoch 082]  average training loss: 4281.8351
cellbender:remove-background: [epoch 083]  average training loss: 4282.3708
cellbender:remove-background: [epoch 084]  average training loss: 4274.6806
cellbender:remove-background: [epoch 085]  average training loss: 4280.5415
cellbender:remove-background: [epoch 085] average test loss: 4214.2495
cellbender:remove-background: [epoch 086]  average training loss: 4281.8581
cellbender:remove-background: [epoch 087]  average training loss: 4273.8128
cellbender:remove-background: [epoch 088]  average training loss: 4271.9668
cellbender:remove-background: [epoch 089]  average training loss: 4292.3643
cellbender:remove-background: [epoch 090]  average training loss: 4294.1792
cellbender:remove-background: [epoch 090] average test loss: 4307.9138
cellbender:remove-background: [epoch 091]  average training loss: 4290.7343
cellbender:remove-background: [epoch 092]  average training loss: 4288.2035
cellbender:remove-background: [epoch 093]  average training loss: 4288.4948
cellbender:remove-background: [epoch 094]  average training loss: 4296.5515
cellbender:remove-background: [epoch 095]  average training loss: 4283.4511
cellbender:remove-background: [epoch 095] average test loss: 4293.9871
cellbender:remove-background: [epoch 096]  average training loss: 4299.0551
cellbender:remove-background: [epoch 097]  average training loss: 4298.0186
cellbender:remove-background: [epoch 098]  average training loss: 4323.8300
cellbender:remove-background: [epoch 099]  average training loss: 4295.1007
cellbender:remove-background: [epoch 100]  average training loss: 4296.1755
cellbender:remove-background: [epoch 100] average test loss: 4270.7746
cellbender:remove-background: [epoch 101]  average training loss: 4278.1395
cellbender:remove-background: [epoch 102]  average training loss: 4297.2065
cellbender:remove-background: [epoch 103]  average training loss: 4300.3908
cellbender:remove-background: [epoch 104]  average training loss: 4288.5780
cellbender:remove-background: [epoch 105]  average training loss: 4283.8815
cellbender:remove-background: [epoch 105] average test loss: 4313.0919
cellbender:remove-background: [epoch 106]  average training loss: 4295.0060
cellbender:remove-background: [epoch 107]  average training loss: 4295.2841
cellbender:remove-background: [epoch 108]  average training loss: 4315.8267
cellbender:remove-background: [epoch 109]  average training loss: 4283.1269
cellbender:remove-background: [epoch 110]  average training loss: 4305.1644
cellbender:remove-background: [epoch 110] average test loss: 4286.2925
cellbender:remove-background: [epoch 111]  average training loss: 4292.7404
cellbender:remove-background: [epoch 112]  average training loss: 4272.0145
cellbender:remove-background: [epoch 113]  average training loss: 4286.3130
cellbender:remove-background: [epoch 114]  average training loss: 4280.0374
cellbender:remove-background: [epoch 115]  average training loss: 4283.4631
cellbender:remove-background: [epoch 115] average test loss: 4266.0272
cellbender:remove-background: [epoch 116]  average training loss: 4281.4384
cellbender:remove-background: [epoch 117]  average training loss: 4297.1786
cellbender:remove-background: [epoch 118]  average training loss: 4292.0354
cellbender:remove-background: [epoch 119]  average training loss: 4272.2678
cellbender:remove-background: [epoch 120]  average training loss: 4283.5037
cellbender:remove-background: [epoch 120] average test loss: 4256.4466
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/2083-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: [epoch 121]  average training loss: 4290.5028
cellbender:remove-background: [epoch 122]  average training loss: 4265.4832
cellbender:remove-background: [epoch 123]  average training loss: 4276.3421
cellbender:remove-background: [epoch 124]  average training loss: 4273.7968
cellbender:remove-background: [epoch 125]  average training loss: 4278.2954
cellbender:remove-background: [epoch 125] average test loss: 4256.3942
cellbender:remove-background: [epoch 126]  average training loss: 4267.3805
cellbender:remove-background: [epoch 127]  average training loss: 4297.4557
cellbender:remove-background: [epoch 128]  average training loss: 4277.8593
cellbender:remove-background: [epoch 129]  average training loss: 4281.1334
cellbender:remove-background: [epoch 130]  average training loss: 4281.2348
cellbender:remove-background: [epoch 130] average test loss: 4279.3648
cellbender:remove-background: [epoch 131]  average training loss: 4290.7688
cellbender:remove-background: [epoch 132]  average training loss: 4265.6591
cellbender:remove-background: [epoch 133]  average training loss: 4270.3994
cellbender:remove-background: [epoch 134]  average training loss: 4272.5233
cellbender:remove-background: [epoch 135]  average training loss: 4269.6857
cellbender:remove-background: [epoch 135] average test loss: 4271.4281
cellbender:remove-background: [epoch 136]  average training loss: 4272.1657
cellbender:remove-background: [epoch 137]  average training loss: 4280.5787
cellbender:remove-background: [epoch 138]  average training loss: 4262.6880
cellbender:remove-background: [epoch 139]  average training loss: 4289.1758
cellbender:remove-background: [epoch 140]  average training loss: 4280.5612
cellbender:remove-background: [epoch 140] average test loss: 4309.9352
cellbender:remove-background: [epoch 141]  average training loss: 4254.7867
cellbender:remove-background: [epoch 142]  average training loss: 4293.1776
cellbender:remove-background: [epoch 143]  average training loss: 4269.6569
cellbender:remove-background: [epoch 144]  average training loss: 4261.5586
cellbender:remove-background: [epoch 145]  average training loss: 4280.6860
cellbender:remove-background: [epoch 145] average test loss: 4258.0830
cellbender:remove-background: [epoch 146]  average training loss: 4281.0200
cellbender:remove-background: [epoch 147]  average training loss: 4295.8723
cellbender:remove-background: [epoch 148]  average training loss: 4261.0259
cellbender:remove-background: [epoch 149]  average training loss: 4278.2227
cellbender:remove-background: [epoch 150]  average training loss: 4254.7669
cellbender:remove-background: [epoch 150] average test loss: 4351.6409
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/2083-Bipolar-DLPFC/ckpt.tar.gz
cellbender:remove-background: 2024-06-06 15:16:10
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmpjuh_dcqc
cellbender:remove-background: Successfully unpacked tarball to /tmp/tmpjuh_dcqc
/tmp/tmpjuh_dcqc/4dbed8f123_random.pyro
/tmp/tmpjuh_dcqc/4dbed8f123_random.cuda
/tmp/tmpjuh_dcqc/4dbed8f123_model.torch
/tmp/tmpjuh_dcqc/4dbed8f123_optim.torch
/tmp/tmpjuh_dcqc/4dbed8f123_optim.pyro
/tmp/tmpjuh_dcqc/4dbed8f123_params.pyro
/tmp/tmpjuh_dcqc/4dbed8f123_train.loaderstate
/tmp/tmpjuh_dcqc/4dbed8f123_test.loaderstate
/tmp/tmpjuh_dcqc/4dbed8f123_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 (1/101)
cellbender:remove-background:     [0.04 mins per chunk]
cellbender:remove-background: Working on chunk (2/101)
cellbender:remove-background: Working on chunk (3/101)
cellbender:remove-background: Working on chunk (4/101)
cellbender:remove-background: Working on chunk (5/101)
cellbender:remove-background: Working on chunk (6/101)
cellbender:remove-background: Working on chunk (7/101)
cellbender:remove-background: Working on chunk (8/101)
cellbender:remove-background: Working on chunk (9/101)
cellbender:remove-background: Working on chunk (10/101)
cellbender:remove-background: Working on chunk (11/101)
cellbender:remove-background: Working on chunk (12/101)
cellbender:remove-background: Working on chunk (13/101)
cellbender:remove-background: Working on chunk (14/101)
cellbender:remove-background: Working on chunk (15/101)
cellbender:remove-background: Working on chunk (16/101)
cellbender:remove-background: Working on chunk (17/101)
cellbender:remove-background: Working on chunk (18/101)
cellbender:remove-background: Working on chunk (19/101)
cellbender:remove-background: Working on chunk (20/101)
cellbender:remove-background: Working on chunk (21/101)
cellbender:remove-background: Working on chunk (22/101)
cellbender:remove-background: Working on chunk (23/101)
cellbender:remove-background: Working on chunk (24/101)
cellbender:remove-background: Working on chunk (25/101)
cellbender:remove-background: Working on chunk (26/101)
cellbender:remove-background: Working on chunk (27/101)
cellbender:remove-background: Working on chunk (28/101)
cellbender:remove-background: Working on chunk (29/101)
cellbender:remove-background: Working on chunk (30/101)
cellbender:remove-background: Working on chunk (31/101)
cellbender:remove-background: Working on chunk (32/101)
cellbender:remove-background: Working on chunk (33/101)
cellbender:remove-background: Working on chunk (34/101)
cellbender:remove-background: Working on chunk (35/101)
cellbender:remove-background: Working on chunk (36/101)
cellbender:remove-background: Working on chunk (37/101)
cellbender:remove-background: Working on chunk (38/101)
cellbender:remove-background: Working on chunk (39/101)
cellbender:remove-background: Working on chunk (40/101)
cellbender:remove-background: Working on chunk (41/101)
cellbender:remove-background: Working on chunk (42/101)
cellbender:remove-background: Working on chunk (43/101)
cellbender:remove-background: Working on chunk (44/101)
cellbender:remove-background: Working on chunk (45/101)
cellbender:remove-background: Working on chunk (46/101)
cellbender:remove-background: Working on chunk (47/101)
cellbender:remove-background: Working on chunk (48/101)
cellbender:remove-background: Working on chunk (49/101)
cellbender:remove-background: Working on chunk (50/101)
cellbender:remove-background: Working on chunk (51/101)
cellbender:remove-background: Working on chunk (52/101)
cellbender:remove-background: Working on chunk (53/101)
cellbender:remove-background: Working on chunk (54/101)
cellbender:remove-background: Working on chunk (55/101)
cellbender:remove-background: Working on chunk (56/101)
cellbender:remove-background: Working on chunk (57/101)
cellbender:remove-background: Working on chunk (58/101)
cellbender:remove-background: Working on chunk (59/101)
cellbender:remove-background: Working on chunk (60/101)
cellbender:remove-background: Working on chunk (61/101)
cellbender:remove-background: Working on chunk (62/101)
cellbender:remove-background: Working on chunk (63/101)
cellbender:remove-background: Working on chunk (64/101)
cellbender:remove-background: Working on chunk (65/101)
cellbender:remove-background: Working on chunk (66/101)
cellbender:remove-background: Working on chunk (67/101)
cellbender:remove-background: Working on chunk (68/101)
cellbender:remove-background: Working on chunk (69/101)
cellbender:remove-background: Working on chunk (70/101)
cellbender:remove-background: Working on chunk (71/101)
cellbender:remove-background: Working on chunk (72/101)
cellbender:remove-background: Working on chunk (73/101)
cellbender:remove-background: Working on chunk (74/101)
cellbender:remove-background: Working on chunk (75/101)
cellbender:remove-background: Working on chunk (76/101)
cellbender:remove-background: Working on chunk (77/101)
cellbender:remove-background: Working on chunk (78/101)
cellbender:remove-background: Working on chunk (79/101)
cellbender:remove-background: Working on chunk (80/101)
cellbender:remove-background: Working on chunk (81/101)
cellbender:remove-background: Working on chunk (82/101)
cellbender:remove-background: Working on chunk (83/101)
cellbender:remove-background: Working on chunk (84/101)
cellbender:remove-background: Working on chunk (85/101)
cellbender:remove-background: Working on chunk (86/101)
cellbender:remove-background: Working on chunk (87/101)
cellbender:remove-background: Working on chunk (88/101)
cellbender:remove-background: Working on chunk (89/101)
cellbender:remove-background: Working on chunk (90/101)
cellbender:remove-background: Working on chunk (91/101)
cellbender:remove-background: Working on chunk (92/101)
cellbender:remove-background: Working on chunk (93/101)
cellbender:remove-background: Working on chunk (94/101)
cellbender:remove-background: Working on chunk (95/101)
cellbender:remove-background: Working on chunk (96/101)
cellbender:remove-background: Working on chunk (97/101)
cellbender:remove-background: Working on chunk (98/101)
cellbender:remove-background: Working on chunk (99/101)
cellbender:remove-background: Working on chunk (100/101)
cellbender:remove-background: Working on chunk (101/101)
cellbender:remove-background: Writing full posterior to /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-DLPFC/2083-Bipolar-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/2083-Bipolar-DLPFC/2083-Bipolar-DLPFC.cellbender.output_posterior.h5
cellbender:remove-background: Added posterior object to checkpoint file.
cellbender:remove-background: 2024-06-06 15:23:24

cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-DLPFC/2083-Bipolar-DLPFC.cellbender.output.pdf
cellbender:remove-background: Saved cell barcodes in /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/2083-Bipolar-DLPFC/2083-Bipolar-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:     [3.36 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 15:48:11 Total MCKP estimation time = 1431.31 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/2083-Bipolar-DLPFC/2083-Bipolar-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/2083-Bipolar-DLPFC/2083-Bipolar-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/2083-Bipolar-DLPFC/2083-Bipolar-DLPFC.cellbender.output_metrics.csv
Traceback (most recent call last):
  File "/home/users/guozy/miniconda3/envs/cellbender/bin/jupyter-nbconvert", line 5, in <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    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 <module>
    ) 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 <module>
    from nbconvert.nbconvertapp import main
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/__init__.py", line 5, in <module>
    from .exporters import *
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/__init__.py", line 1, in <module>
    from .asciidoc import ASCIIDocExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/asciidoc.py", line 9, in <module>
    from .templateexporter import TemplateExporter
  File "/home/users/guozy/miniconda3/envs/cellbender/lib/python3.7/site-packages/nbconvert/exporters/templateexporter.py", line 25, in <module>
    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 <module>
    ) 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/2083-Bipolar-DLPFC/2083-Bipolar-DLPFC.cellbender.output_report.html'

cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-06-06 15:48:42