cellbender:remove-background: Command: cellbender remove-background --input /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/inputs/1672-Schizophrenia-Hippocampus.raw_feature_bc_matrix.h5 --output /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1672-Schizophrenia-Hippocampus/1672-Schizophrenia-Hippocampus.cellbender.output.h5 --cuda --expected-cells 5494 --total-droplets-included 20000 --fpr 0.01 --epochs 150 cellbender:remove-background: CellBender 0.3.0 cellbender:remove-background: (Workflow hash ce6a5a000b) cellbender:remove-background: 2024-06-06 15:56:03 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/1672-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: 32217 features have nonzero counts. cellbender:remove-background: Prior on counts for cells is 5854 cellbender:remove-background: Prior on counts for empty droplets is 213 cellbender:remove-background: Excluding 10409 features that are estimated to have <= 0.1 background counts in cells. cellbender:remove-background: Including 21808 features in the analysis. cellbender:remove-background: Trimming barcodes for inference. cellbender:remove-background: Excluding barcodes with counts below 106 cellbender:remove-background: Using 5494 probable cell barcodes, plus an additional 14506 barcodes, and 16559 empty droplets. cellbender:remove-background: Largest surely-empty droplet has 210 UMI counts. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp77_4ki1j cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp77_4ki1j /tmp/tmp77_4ki1j/ce6a5a000b_random.pyro /tmp/tmp77_4ki1j/ce6a5a000b_random.cuda /tmp/tmp77_4ki1j/ce6a5a000b_model.torch /tmp/tmp77_4ki1j/ce6a5a000b_optim.torch /tmp/tmp77_4ki1j/ce6a5a000b_optim.pyro /tmp/tmp77_4ki1j/ce6a5a000b_params.pyro /tmp/tmp77_4ki1j/ce6a5a000b_train.loaderstate /tmp/tmp77_4ki1j/ce6a5a000b_test.loaderstate /tmp/tmp77_4ki1j/ce6a5a000b_args.npy /tmp/tmp77_4ki1j/posterior.h5 cellbender:remove-background: Loaded partially-trained checkpoint from ckpt.tar.gz cellbender:remove-background: Checkpoint loaded successfully. cellbender:remove-background: Running inference... cellbender:remove-background: 2024-06-06 15:56:31 cellbender:remove-background: Inference procedure complete. cellbender:remove-background: Attempting to unpack tarball "ckpt.tar.gz" to /tmp/tmp97u7322k cellbender:remove-background: Successfully unpacked tarball to /tmp/tmp97u7322k /tmp/tmp97u7322k/ce6a5a000b_random.pyro /tmp/tmp97u7322k/ce6a5a000b_random.cuda /tmp/tmp97u7322k/ce6a5a000b_model.torch /tmp/tmp97u7322k/ce6a5a000b_optim.torch /tmp/tmp97u7322k/ce6a5a000b_optim.pyro /tmp/tmp97u7322k/ce6a5a000b_params.pyro /tmp/tmp97u7322k/ce6a5a000b_train.loaderstate /tmp/tmp97u7322k/ce6a5a000b_test.loaderstate /tmp/tmp97u7322k/ce6a5a000b_args.npy /tmp/tmp97u7322k/posterior.h5 cellbender:remove-background: Loaded pre-computed posterior from posterior.h5 cellbender:remove-background: 2024-06-06 15:56:50 cellbender:remove-background: Saved summary plots as /oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/01-cellbender/outputs/1672-Schizophrenia-Hippocampus/1672-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/1672-Schizophrenia-Hippocampus/1672-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: [1.93 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 16:10:41 Total MCKP estimation time = 787.94 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/1672-Schizophrenia-Hippocampus/1672-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/1672-Schizophrenia-Hippocampus/1672-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/1672-Schizophrenia-Hippocampus/1672-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/1672-Schizophrenia-Hippocampus/1672-Schizophrenia-Hippocampus.cellbender.output_report.html' cellbender:remove-background: Completed remove-background. cellbender:remove-background: 2024-06-06 16:11:07