cellbender v3.0 doesn't generate most of the output files, but doesn't have any errors
cswoboda opened this issue · 1 comments
Hello! Amazing tool. I've been using an older form of cellbender, and installed a newer form on our universities computational cluster in order to make use of the new output files. However, the run successfully completes, but is missing the metrics output file, and the html summary. Here's the full run. Conda activate cellbender03 should be activating version 3.0.
#LSBATCH: User input
#BSUB -L /bin/bash
#BSUB -W 10000
#BSUB -n 2
#BSUB -M 32000
#BSUB -q gpu-v100
#BSUB -gpu "num=1"
#BSUB -R "span[hosts=1]"
module load anaconda3
module load cuda/10.1
conda init
conda activate cellbender03
cellbender remove-background --input /data/cellbender-inputs/Control3_raw_feature_bc_matrix.h5 --output /data/cellbender-outs/Control3_cellbender_corrected.h5 --cuda --fpr 0.01 --epochs 150
Successfully completed.
Resource usage summary:
CPU time : 6978.86 sec.
Max Memory : 4443 MB
Average Memory : 3590.09 MB
Total Requested Memory : 32000.00 MB
Delta Memory : 27557.00 MB
Max Swap : 2 MB
Max Processes : 5
Max Threads : 47
Run time : 3654 sec.
Turnaround time : 3664 sec.
The output (if any) follows:
cellbender:remove-background: Command:
cellbender remove-background --input /data/cellbender-inputs/Control3_raw_feature_bc_matrix.h5 --output /data/cellbender-outs/Control3_cellbender_corrected.h5 --cuda --fpr 0.01 --epochs 150
cellbender:remove-background: 2024-05-08 13:59:08
cellbender:remove-background: Running remove-background
cellbender:remove-background: Loading data from file /data/cellbender-inputs/Control3_raw_feature_bc_matrix.h5
cellbender:remove-background: CellRanger v3 format
cellbender:remove-background: Trimming dataset for inference.
cellbender:remove-background: Including 26514 genes that have nonzero counts.
cellbender:remove-background: Prior on counts in empty droplets is 734
cellbender:remove-background: Prior on counts for cells is 7208
cellbender:remove-background: Excluding barcodes with counts below 367
cellbender:remove-background: Using 11265 probable cell barcodes, plus an additional 13735 barcodes, and 57467 empty droplets.
cellbender:remove-background: Largest surely-empty droplet has 895 UMI counts.
cellbender:remove-background: Running inference...
cellbender:remove-background: [epoch 001] average training loss: 5347.6744
cellbender:remove-background: [epoch 002] average training loss: 4374.9999 (17.9 seconds per epoch)
cellbender:remove-background: [epoch 003] average training loss: 4150.1302
cellbender:remove-background: [epoch 004] average training loss: 4071.7820
cellbender:remove-background: [epoch 005] average training loss: 4022.4898
cellbender:remove-background: [epoch 005] average test loss: 3973.0700
cellbender:remove-background: [epoch 006] average training loss: 3964.3670
cellbender:remove-background: [epoch 007] average training loss: 3945.6980
cellbender:remove-background: [epoch 008] average training loss: 3941.6377
cellbender:remove-background: [epoch 009] average training loss: 3928.8291
cellbender:remove-background: [epoch 010] average training loss: 3924.5242
cellbender:remove-background: [epoch 010] average test loss: 3912.0716
cellbender:remove-background: [epoch 011] average training loss: 3927.8465
cellbender:remove-background: [epoch 012] average training loss: 3922.8986
cellbender:remove-background: [epoch 013] average training loss: 3915.8853
cellbender:remove-background: [epoch 014] average training loss: 3914.1459
cellbender:remove-background: [epoch 015] average training loss: 3916.1158
cellbender:remove-background: [epoch 015] average test loss: 3902.9800
cellbender:remove-background: [epoch 016] average training loss: 3904.8473
cellbender:remove-background: [epoch 017] average training loss: 3855.8081
cellbender:remove-background: [epoch 018] average training loss: 3834.8974
cellbender:remove-background: [epoch 019] average training loss: 3823.8857
cellbender:remove-background: [epoch 020] average training loss: 3810.1713
cellbender:remove-background: [epoch 020] average test loss: 3789.7216
cellbender:remove-background: [epoch 021] average training loss: 3797.5985
cellbender:remove-background: [epoch 022] average training loss: 3791.8554
cellbender:remove-background: [epoch 023] average training loss: 3781.5092
cellbender:remove-background: [epoch 024] average training loss: 3772.7266
cellbender:remove-background: [epoch 025] average training loss: 3768.8021
cellbender:remove-background: [epoch 025] average test loss: 3755.8819
cellbender:remove-background: [epoch 026] average training loss: 3764.1117
cellbender:remove-background: [epoch 027] average training loss: 3759.5244
cellbender:remove-background: [epoch 028] average training loss: 3756.0278
cellbender:remove-background: [epoch 029] average training loss: 3749.2436
cellbender:remove-background: [epoch 030] average training loss: 3748.2135
cellbender:remove-background: [epoch 030] average test loss: 3734.8273
cellbender:remove-background: [epoch 031] average training loss: 3743.8361
cellbender:remove-background: [epoch 032] average training loss: 3740.2271
cellbender:remove-background: [epoch 033] average training loss: 3737.6663
cellbender:remove-background: [epoch 034] average training loss: 3735.4438
cellbender:remove-background: [epoch 035] average training loss: 3733.5313
cellbender:remove-background: [epoch 035] average test loss: 3727.7530
cellbender:remove-background: [epoch 036] average training loss: 3731.4035
cellbender:remove-background: [epoch 037] average training loss: 3729.3962
cellbender:remove-background: [epoch 038] average training loss: 3726.4831
cellbender:remove-background: [epoch 039] average training loss: 3720.7083
cellbender:remove-background: [epoch 040] average training loss: 3718.1618
cellbender:remove-background: [epoch 040] average test loss: 3709.2272
cellbender:remove-background: [epoch 041] average training loss: 3715.1231
cellbender:remove-background: [epoch 042] average training loss: 3712.0890
cellbender:remove-background: [epoch 043] average training loss: 3709.8681
cellbender:remove-background: [epoch 044] average training loss: 3707.4289
cellbender:remove-background: [epoch 045] average training loss: 3704.8866
cellbender:remove-background: [epoch 045] average test loss: 3694.5016
cellbender:remove-background: [epoch 046] average training loss: 3701.9518
cellbender:remove-background: [epoch 047] average training loss: 3698.5169
cellbender:remove-background: [epoch 048] average training loss: 3697.1491
cellbender:remove-background: [epoch 049] average training loss: 3696.5791
cellbender:remove-background: [epoch 050] average training loss: 3694.7941
cellbender:remove-background: [epoch 050] average test loss: 3688.0470
cellbender:remove-background: [epoch 051] average training loss: 3692.0785
cellbender:remove-background: [epoch 052] average training loss: 3689.6233
cellbender:remove-background: [epoch 053] average training loss: 3688.2671
cellbender:remove-background: [epoch 054] average training loss: 3683.3029
cellbender:remove-background: [epoch 055] average training loss: 3680.9655
cellbender:remove-background: [epoch 055] average test loss: 3672.7299
cellbender:remove-background: [epoch 056] average training loss: 3679.0682
cellbender:remove-background: [epoch 057] average training loss: 3677.7769
cellbender:remove-background: [epoch 058] average training loss: 3677.3356
cellbender:remove-background: [epoch 059] average training loss: 3680.4859
cellbender:remove-background: [epoch 060] average training loss: 3678.1786
cellbender:remove-background: [epoch 060] average test loss: 3673.8649
cellbender:remove-background: [epoch 061] average training loss: 3682.1170
cellbender:remove-background: [epoch 062] average training loss: 3688.7590
cellbender:remove-background: [epoch 063] average training loss: 3682.2961
cellbender:remove-background: [epoch 064] average training loss: 3679.7014
cellbender:remove-background: [epoch 065] average training loss: 3681.1230
cellbender:remove-background: [epoch 065] average test loss: 3666.8923
cellbender:remove-background: [epoch 066] average training loss: 3687.8158
cellbender:remove-background: [epoch 067] average training loss: 3679.9039
cellbender:remove-background: [epoch 068] average training loss: 3676.7172
cellbender:remove-background: [epoch 069] average training loss: 3679.4219
cellbender:remove-background: [epoch 070] average training loss: 3686.8794
cellbender:remove-background: [epoch 070] average test loss: 3681.0164
cellbender:remove-background: [epoch 071] average training loss: 3683.1021
cellbender:remove-background: [epoch 072] average training loss: 3681.1868
cellbender:remove-background: [epoch 073] average training loss: 3679.5698
cellbender:remove-background: [epoch 074] average training loss: 3679.2296
cellbender:remove-background: [epoch 075] average training loss: 3676.3138
cellbender:remove-background: [epoch 075] average test loss: 3682.0727
cellbender:remove-background: [epoch 076] average training loss: 3683.8161
cellbender:remove-background: [epoch 077] average training loss: 3673.5035
cellbender:remove-background: [epoch 078] average training loss: 3675.6524
cellbender:remove-background: [epoch 079] average training loss: 3673.3778
cellbender:remove-background: [epoch 080] average training loss: 3670.5102
cellbender:remove-background: [epoch 080] average test loss: 3677.3251
cellbender:remove-background: [epoch 081] average training loss: 3672.2921
cellbender:remove-background: [epoch 082] average training loss: 3669.9947
cellbender:remove-background: [epoch 083] average training loss: 3678.6621
cellbender:remove-background: [epoch 084] average training loss: 3665.4948
cellbender:remove-background: [epoch 085] average training loss: 3665.8716
cellbender:remove-background: [epoch 085] average test loss: 3696.9737
cellbender:remove-background: [epoch 086] average training loss: 3664.5997
cellbender:remove-background: [epoch 087] average training loss: 3664.0920
cellbender:remove-background: [epoch 088] average training loss: 3662.7945
cellbender:remove-background: [epoch 089] average training loss: 3662.9274
cellbender:remove-background: [epoch 090] average training loss: 3661.2173
cellbender:remove-background: [epoch 090] average test loss: 3679.8258
cellbender:remove-background: [epoch 091] average training loss: 3660.9971
cellbender:remove-background: [epoch 092] average training loss: 3659.0103
cellbender:remove-background: [epoch 093] average training loss: 3658.9914
cellbender:remove-background: [epoch 094] average training loss: 3659.7554
cellbender:remove-background: [epoch 095] average training loss: 3658.9406
cellbender:remove-background: [epoch 095] average test loss: 3670.1030
cellbender:remove-background: [epoch 096] average training loss: 3659.8987
cellbender:remove-background: [epoch 097] average training loss: 3656.0618
cellbender:remove-background: [epoch 098] average training loss: 3658.0610
cellbender:remove-background: [epoch 099] average training loss: 3656.7072
cellbender:remove-background: [epoch 100] average training loss: 3655.7021
cellbender:remove-background: [epoch 100] average test loss: 3665.2102
cellbender:remove-background: [epoch 101] average training loss: 3655.3289
cellbender:remove-background: [epoch 102] average training loss: 3655.0225
cellbender:remove-background: [epoch 103] average training loss: 3653.9965
cellbender:remove-background: [epoch 104] average training loss: 3654.9325
cellbender:remove-background: [epoch 105] average training loss: 3655.3952
cellbender:remove-background: [epoch 105] average test loss: 3663.0204
cellbender:remove-background: [epoch 106] average training loss: 3653.4235
cellbender:remove-background: [epoch 107] average training loss: 3653.4157
cellbender:remove-background: [epoch 108] average training loss: 3654.6665
cellbender:remove-background: [epoch 109] average training loss: 3652.7165
cellbender:remove-background: [epoch 110] average training loss: 3652.5705
cellbender:remove-background: [epoch 110] average test loss: 3657.3691
cellbender:remove-background: [epoch 111] average training loss: 3653.1412
cellbender:remove-background: [epoch 112] average training loss: 3651.6951
cellbender:remove-background: [epoch 113] average training loss: 3651.6466
cellbender:remove-background: [epoch 114] average training loss: 3652.0693
cellbender:remove-background: [epoch 115] average training loss: 3650.7289
cellbender:remove-background: [epoch 115] average test loss: 3658.8186
cellbender:remove-background: [epoch 116] average training loss: 3651.3572
cellbender:remove-background: [epoch 117] average training loss: 3649.8415
cellbender:remove-background: [epoch 118] average training loss: 3650.6730
cellbender:remove-background: [epoch 119] average training loss: 3649.3739
cellbender:remove-background: [epoch 120] average training loss: 3651.6230
cellbender:remove-background: [epoch 120] average test loss: 3651.8215
cellbender:remove-background: [epoch 121] average training loss: 3650.3769
cellbender:remove-background: [epoch 122] average training loss: 3650.4961
cellbender:remove-background: [epoch 123] average training loss: 3649.4580
cellbender:remove-background: [epoch 124] average training loss: 3648.7183
cellbender:remove-background: [epoch 125] average training loss: 3648.5544
cellbender:remove-background: [epoch 125] average test loss: 3651.8633
cellbender:remove-background: [epoch 126] average training loss: 3649.0808
cellbender:remove-background: [epoch 127] average training loss: 3649.6059
cellbender:remove-background: [epoch 128] average training loss: 3648.7723
cellbender:remove-background: [epoch 129] average training loss: 3649.6041
cellbender:remove-background: [epoch 130] average training loss: 3648.0021
cellbender:remove-background: [epoch 130] average test loss: 3651.2660
cellbender:remove-background: [epoch 131] average training loss: 3647.5236
cellbender:remove-background: [epoch 132] average training loss: 3645.7249
cellbender:remove-background: [epoch 133] average training loss: 3648.4092
cellbender:remove-background: [epoch 134] average training loss: 3647.1331
cellbender:remove-background: [epoch 135] average training loss: 3647.2023
cellbender:remove-background: [epoch 135] average test loss: 3648.2057
cellbender:remove-background: [epoch 136] average training loss: 3647.3049
cellbender:remove-background: [epoch 137] average training loss: 3646.0022
cellbender:remove-background: [epoch 138] average training loss: 3647.8876
cellbender:remove-background: [epoch 139] average training loss: 3646.8940
cellbender:remove-background: [epoch 140] average training loss: 3647.3962
cellbender:remove-background: [epoch 140] average test loss: 3648.7842
cellbender:remove-background: [epoch 141] average training loss: 3647.2094
cellbender:remove-background: [epoch 142] average training loss: 3645.5910
cellbender:remove-background: [epoch 143] average training loss: 3647.5731
cellbender:remove-background: [epoch 144] average training loss: 3647.6937
cellbender:remove-background: [epoch 145] average training loss: 3646.7066
cellbender:remove-background: [epoch 145] average test loss: 3649.2645
cellbender:remove-background: [epoch 146] average training loss: 3646.4411
cellbender:remove-background: [epoch 147] average training loss: 3646.0331
cellbender:remove-background: [epoch 148] average training loss: 3646.6610
cellbender:remove-background: [epoch 149] average training loss: 3646.0654
cellbender:remove-background: [epoch 150] average training loss: 3645.8741
cellbender:remove-background: [epoch 150] average test loss: 3651.3797
cellbender:remove-background: Inference procedure complete.
cellbender:remove-background: 2024-05-08 14:45:48
cellbender:remove-background: Preparing to write outputs to file...
cellbender:remove-background: Optimal posterior regularization factor = 2.37
cellbender:remove-background: Succeeded in writing CellRanger v3 format output to file /data/cellbender-outs/Control3_cellbender_corrected.h5
cellbender:remove-background: Succeeded in writing CellRanger v3 format output to file /data/cellbender-outs/Control3_cellbender_corrected_filtered.h5
cellbender:remove-background: Saved cell barcodes in /data/cellbender-outs/Control3_cellbender_corrected_cell_barcodes.csv
cellbender:remove-background: Saved summary plots as /data/cellbender-outs/Control3_cellbender_corrected.pdf
cellbender:remove-background: Completed remove-background.
cellbender:remove-background: 2024-05-08 14:59:50