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broadinstitute / CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
https://cellbender.rtfd.io
BSD 3-Clause "New" or "Revised" License
271 stars 50 forks source link

Determine which version of cellbender was used for a run #335

Open chris-rands opened 4 months ago

chris-rands commented 4 months ago

Hi @sjfleming, thanks again for cellbender. Prior to cellbender 0.3.0 release, I can't figure out what version of cellbender was used for a particular run. How can I determine this from the cellbender output files if 0.2.2 / 0.2.1 / 0.2.0 / 0.1.0 was used? Thank you

The output directory contains the following files from cellbender and cellranger:

cellbender_feature_bc_matrix_cell_barcodes.csv  filtered_feature_bc_matrix     raw_dropkick.h5ad
cellbender_feature_bc_matrix_filtered.h5        filtered_feature_bc_matrix.h5  raw_dropkick_label-score.csv
cellbender_feature_bc_matrix.h5                 filtered.h5ad                  raw_feature_bc_matrix
cellbender_feature_bc_matrix.log                filtered_score.png             raw_feature_bc_matrix.h5
cellbender_feature_bc_matrix.pdf                metrics_summary.csv            raw.h5ad
filtered_coef.png                               molecule_info.h5               raw_score.png
filtered_dropkick.h5ad                          __pycache__                    web_summary.html
filtered_dropkick_label-score.csv               raw_coef.png

Here is the log file (paths edited):

cellbender:remove-background: Command:
cellbender remove-background --input /path/in/ --output /path/out/ --expected-cells 5000
cellbender:remove-background: 2022-10-17 12:57:24
cellbender:remove-background: Running remove-background
cellbender:remove-background: Loading data from file /path/raw_feature_bc_matrix.h5
cellbender:remove-background: CellRanger v3 format
cellbender:remove-background: Trimming dataset for inference.
cellbender:remove-background: Including 33092 genes that have nonzero counts.
cellbender:remove-background: Prior on counts in empty droplets is 896
cellbender:remove-background: Prior on counts for cells is 3254
cellbender:remove-background: Excluding barcodes with counts below 448
cellbender:remove-background: Using 5000 probable cell barcodes, plus an additional 20000 barcodes, and 57295 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 987 UMI counts.
cellbender:remove-background: Running inference...
cellbender:remove-background: [epoch 001]  average training loss: 4265.3160
cellbender:remove-background: [epoch 002]  average training loss: 3909.4253  (1688.0 seconds per epoch)
cellbender:remove-background: [epoch 003]  average training loss: 3855.3324
cellbender:remove-background: [epoch 004]  average training loss: 3829.3648
cellbender:remove-background: [epoch 005]  average training loss: 3805.5388
cellbender:remove-background: [epoch 005] average test loss: 3800.5839
cellbender:remove-background: [epoch 006]  average training loss: 3791.5532
cellbender:remove-background: [epoch 007]  average training loss: 3771.5445
cellbender:remove-background: [epoch 008]  average training loss: 3753.4644
cellbender:remove-background: [epoch 009]  average training loss: 3753.8093
cellbender:remove-background: [epoch 010]  average training loss: 3752.7755
cellbender:remove-background: [epoch 010] average test loss: 3748.1770
cellbender:remove-background: [epoch 011]  average training loss: 3752.0685
cellbender:remove-background: [epoch 012]  average training loss: 3750.0965
cellbender:remove-background: [epoch 013]  average training loss: 3749.0988
cellbender:remove-background: [epoch 014]  average training loss: 3750.8217
cellbender:remove-background: [epoch 015]  average training loss: 3750.5404
cellbender:remove-background: [epoch 015] average test loss: 3744.3029
cellbender:remove-background: [epoch 016]  average training loss: 3747.9282
cellbender:remove-background: [epoch 017]  average training loss: 3758.9465
cellbender:remove-background: [epoch 018]  average training loss: 3762.6666
cellbender:remove-background: [epoch 019]  average training loss: 3776.4103
cellbender:remove-background: [epoch 020]  average training loss: 3795.9178
cellbender:remove-background: [epoch 020] average test loss: 3802.8584
cellbender:remove-background: [epoch 021]  average training loss: 3787.9211
cellbender:remove-background: [epoch 022]  average training loss: 3794.3878
cellbender:remove-background: [epoch 023]  average training loss: 3774.7062
cellbender:remove-background: [epoch 024]  average training loss: 3750.1103
cellbender:remove-background: [epoch 025]  average training loss: 3713.3584
cellbender:remove-background: [epoch 025] average test loss: 3707.6313
cellbender:remove-background: [epoch 026]  average training loss: 3687.0070
cellbender:remove-background: [epoch 027]  average training loss: 3662.5635
cellbender:remove-background: [epoch 028]  average training loss: 3645.2235
cellbender:remove-background: [epoch 029]  average training loss: 3642.5422
cellbender:remove-background: [epoch 030]  average training loss: 3648.3656
cellbender:remove-background: [epoch 030] average test loss: 3665.8866
cellbender:remove-background: [epoch 031]  average training loss: 3652.3823
cellbender:remove-background: [epoch 032]  average training loss: 3670.2611
cellbender:remove-background: [epoch 033]  average training loss: 3659.1175
cellbender:remove-background: [epoch 034]  average training loss: 3666.1462
cellbender:remove-background: [epoch 035]  average training loss: 3677.6401
cellbender:remove-background: [epoch 035] average test loss: 3659.1921
cellbender:remove-background: [epoch 036]  average training loss: 3715.7818
cellbender:remove-background: [epoch 037]  average training loss: 3722.2565
cellbender:remove-background: [epoch 038]  average training loss: 3764.0848
cellbender:remove-background: [epoch 039]  average training loss: 3796.1710
cellbender:remove-background: [epoch 040]  average training loss: 3782.1217
cellbender:remove-background: [epoch 040] average test loss: 3665.5906
cellbender:remove-background: [epoch 041]  average training loss: 3784.0067
cellbender:remove-background: [epoch 042]  average training loss: 3804.2374
cellbender:remove-background: [epoch 043]  average training loss: 3804.7661
cellbender:remove-background: [epoch 044]  average training loss: 3797.0048
cellbender:remove-background: [epoch 045]  average training loss: 3771.2863
cellbender:remove-background: [epoch 045] average test loss: 3743.2818
cellbender:remove-background: [epoch 046]  average training loss: 3782.7464
cellbender:remove-background: [epoch 047]  average training loss: 3770.3278
cellbender:remove-background: [epoch 048]  average training loss: 3766.8338
cellbender:remove-background: [epoch 049]  average training loss: 3762.4125
cellbender:remove-background: [epoch 050]  average training loss: 3747.2864
cellbender:remove-background: [epoch 050] average test loss: 3649.0708
cellbender:remove-background: [epoch 051]  average training loss: 3722.5260
cellbender:remove-background: [epoch 052]  average training loss: 3723.0781
cellbender:remove-background: [epoch 053]  average training loss: 3732.5364
cellbender:remove-background: [epoch 054]  average training loss: 3721.9454
cellbender:remove-background: [epoch 055]  average training loss: 3723.7524
cellbender:remove-background: [epoch 055] average test loss: 3651.5183
cellbender:remove-background: [epoch 056]  average training loss: 3734.8043
cellbender:remove-background: [epoch 057]  average training loss: 3738.0000
cellbender:remove-background: [epoch 058]  average training loss: 3748.5659
cellbender:remove-background: [epoch 059]  average training loss: 3744.8675
cellbender:remove-background: [epoch 060]  average training loss: 3725.0074
cellbender:remove-background: [epoch 060] average test loss: 3640.3824
cellbender:remove-background: [epoch 061]  average training loss: 3726.6667
cellbender:remove-background: [epoch 062]  average training loss: 3745.3824
cellbender:remove-background: [epoch 063]  average training loss: 3727.2779
cellbender:remove-background: [epoch 064]  average training loss: 3737.1769
cellbender:remove-background: [epoch 065]  average training loss: 3713.0426
cellbender:remove-background: [epoch 065] average test loss: 3623.5553
cellbender:remove-background: [epoch 066]  average training loss: 3704.2067
cellbender:remove-background: [epoch 067]  average training loss: 3710.9334
cellbender:remove-background: [epoch 068]  average training loss: 3699.2421
cellbender:remove-background: [epoch 069]  average training loss: 3701.2342
cellbender:remove-background: [epoch 070]  average training loss: 3700.1533
cellbender:remove-background: [epoch 070] average test loss: 3635.4410
cellbender:remove-background: [epoch 071]  average training loss: 3705.7550
cellbender:remove-background: [epoch 072]  average training loss: 3710.9476
cellbender:remove-background: [epoch 073]  average training loss: 3700.7985
cellbender:remove-background: [epoch 074]  average training loss: 3700.0685
cellbender:remove-background: [epoch 075]  average training loss: 3697.8404
cellbender:remove-background: [epoch 075] average test loss: 3630.6847
cellbender:remove-background: [epoch 076]  average training loss: 3667.6597
cellbender:remove-background: [epoch 077]  average training loss: 3633.5399
cellbender:remove-background: [epoch 078]  average training loss: 3654.5093
cellbender:remove-background: [epoch 079]  average training loss: 3598.0845
cellbender:remove-background: [epoch 080]  average training loss: 3632.1582
cellbender:remove-background: [epoch 080] average test loss: 3630.1727
cellbender:remove-background: [epoch 081]  average training loss: 3628.9163
cellbender:remove-background: [epoch 082]  average training loss: 3620.8141
cellbender:remove-background: [epoch 083]  average training loss: 3597.8724
cellbender:remove-background: [epoch 084]  average training loss: 3598.7161
cellbender:remove-background: [epoch 085]  average training loss: 3600.7690
cellbender:remove-background: [epoch 085] average test loss: 3625.7554
cellbender:remove-background: [epoch 086]  average training loss: 3608.6537
cellbender:remove-background: [epoch 087]  average training loss: 3658.0685
cellbender:remove-background: [epoch 088]  average training loss: 3651.6844
cellbender:remove-background: [epoch 089]  average training loss: 3657.8512
cellbender:remove-background: [epoch 090]  average training loss: 3659.6286
cellbender:remove-background: [epoch 090] average test loss: 3623.1537
cellbender:remove-background: [epoch 091]  average training loss: 3599.8082
cellbender:remove-background: [epoch 092]  average training loss: 3595.5456
cellbender:remove-background: [epoch 093]  average training loss: 3648.0280
cellbender:remove-background: [epoch 094]  average training loss: 3634.5642
cellbender:remove-background: [epoch 095]  average training loss: 3688.5996
cellbender:remove-background: [epoch 095] average test loss: 3617.0173
cellbender:remove-background: [epoch 096]  average training loss: 3687.5439
cellbender:remove-background: [epoch 097]  average training loss: 3685.1448
cellbender:remove-background: [epoch 098]  average training loss: 3684.8517
cellbender:remove-background: [epoch 099]  average training loss: 3682.8811
cellbender:remove-background: [epoch 100]  average training loss: 3681.8445
cellbender:remove-background: [epoch 100] average test loss: 3616.1717
cellbender:remove-background: [epoch 101]  average training loss: 3680.9919
cellbender:remove-background: [epoch 102]  average training loss: 3681.2664
cellbender:remove-background: [epoch 103]  average training loss: 3682.3400
cellbender:remove-background: [epoch 104]  average training loss: 3680.9696
cellbender:remove-background: [epoch 105]  average training loss: 3681.1928
cellbender:remove-background: [epoch 105] average test loss: 3619.3725
cellbender:remove-background: [epoch 106]  average training loss: 3679.5162
cellbender:remove-background: [epoch 107]  average training loss: 3670.1658
cellbender:remove-background: [epoch 108]  average training loss: 3667.2942
cellbender:remove-background: [epoch 109]  average training loss: 3678.9382
cellbender:remove-background: [epoch 110]  average training loss: 3679.7891
cellbender:remove-background: [epoch 110] average test loss: 3615.7908
cellbender:remove-background: [epoch 111]  average training loss: 3679.4431
cellbender:remove-background: [epoch 112]  average training loss: 3678.3187
cellbender:remove-background: [epoch 113]  average training loss: 3679.4003
cellbender:remove-background: [epoch 114]  average training loss: 3677.2780
cellbender:remove-background: [epoch 115]  average training loss: 3673.6309
cellbender:remove-background: [epoch 115] average test loss: 3618.4050
cellbender:remove-background: [epoch 116]  average training loss: 3677.4807
cellbender:remove-background: [epoch 117]  average training loss: 3672.6315
cellbender:remove-background: [epoch 118]  average training loss: 3665.8363
cellbender:remove-background: [epoch 119]  average training loss: 3658.5780
cellbender:remove-background: [epoch 120]  average training loss: 3660.8785
cellbender:remove-background: [epoch 120] average test loss: 3608.1585
cellbender:remove-background: [epoch 121]  average training loss: 3673.7972
cellbender:remove-background: [epoch 122]  average training loss: 3667.9216
cellbender:remove-background: [epoch 123]  average training loss: 3665.2398
cellbender:remove-background: [epoch 124]  average training loss: 3670.4048
cellbender:remove-background: [epoch 125]  average training loss: 3664.9065
cellbender:remove-background: [epoch 125] average test loss: 3609.7614
cellbender:remove-background: [epoch 126]  average training loss: 3667.8571
cellbender:remove-background: [epoch 127]  average training loss: 3661.2457
cellbender:remove-background: [epoch 128]  average training loss: 3670.8577
cellbender:remove-background: [epoch 129]  average training loss: 3662.1306
cellbender:remove-background: [epoch 130]  average training loss: 3656.8860
cellbender:remove-background: [epoch 130] average test loss: 3608.3925
cellbender:remove-background: [epoch 131]  average training loss: 3658.0988
cellbender:remove-background: [epoch 132]  average training loss: 3658.3424
cellbender:remove-background: [epoch 133]  average training loss: 3656.9031
cellbender:remove-background: [epoch 134]  average training loss: 3655.8860
cellbender:remove-background: [epoch 135]  average training loss: 3656.1560
cellbender:remove-background: [epoch 135] average test loss: 3604.0831
cellbender:remove-background: [epoch 136]  average training loss: 3654.3567
cellbender:remove-background: [epoch 137]  average training loss: 3656.4487
cellbender:remove-background: [epoch 138]  average training loss: 3655.1678
cellbender:remove-background: [epoch 139]  average training loss: 3655.1077
cellbender:remove-background: [epoch 140]  average training loss: 3656.1219
cellbender:remove-background: [epoch 140] average test loss: 3608.2641
cellbender:remove-background: [epoch 141]  average training loss: 3653.6794
cellbender:remove-background: [epoch 142]  average training loss: 3652.2994
cellbender:remove-background: [epoch 143]  average training loss: 3654.8566
cellbender:remove-background: [epoch 144]  average training loss: 3653.6182
cellbender:remove-background: [epoch 145]  average training loss: 3656.2340
cellbender:remove-background: [epoch 145] average test loss: 3605.8882
cellbender:remove-background: [epoch 146]  average training loss: 3653.2946
cellbender:remove-background: [epoch 147]  average training loss: 3654.3019
cellbender:remove-background: [epoch 148]  average training loss: 3652.2255
cellbender:remove-background: [epoch 149]  average training loss: 3652.7143
cellbender:remove-background: [epoch 150]  average training loss: 3652.6361
cellbender:remove-background: [epoch 150] average test loss: 3610.3715
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: Training succeeded
cellbender:remove-background: 2022-10-20 17:45:28
cellbender:remove-background: Preparing to write outputs to file...
cellbender:remove-background: Optimal posterior regularization factor = 1.49
cellbender:remove-background: Succeeded in writing CellRanger v3 format output to file /path/cellbender_feature_bc_matrix.h5
cellbender:remove-background: Succeeded in writing CellRanger v3 format output to file /path/cellbender_feature_bc_matrix_filtered.h5
cellbender:remove-background: Saved cell barcodes in /path/cellbender_feature_bc_matrix_cell_barcodes.csv
cellbender:remove-background: Saved summary plots as /path/cellbender_feature_bc_matrix.pdf
cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2022-10-21 15:21:54