Open manogenome opened 1 month ago
Also, another error message at this step for a different dataset:
Error message from the terminal:
[Thu Jul 25 15:13:38 2024]
Finished job 41.
39 of 43 steps (91%) done
Exiting because a job execution failed. Look above for error message
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-07-25T092757.755271.snakemake.log
Traceback (most recent call last):
File "/opt/conda/envs/cellsnake/bin/cellsnake", line 8, in <module>
sys.exit(main())
File "/opt/conda/envs/cellsnake/lib/python3.9/site-packages/cellsnake/command_line.py", line 381, in main
run_workflow(cli_arguments)
File "/opt/conda/envs/cellsnake/lib/python3.9/site-packages/cellsnake/command_line.py", line 351, in run_workflow
subprocess.check_call(str(snakemake_argument),shell=True)
File "/opt/conda/envs/cellsnake/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'snakemake --retries 5 --rerun-incomplete -k -j 85 -s /opt/conda/envs/cellsnake/lib/python3.9/site-packages/cellsnake/scrna/workflow/Snakefile --configfile=config.yaml --config datafolder=analyses_integrated/seurat/integrated.rds cellsnake_path=/opt/conda/envs/cellsnake/lib/python3.9/site-packages/cellsnake/scrna/ min_molecules=0 singler_ref=BlueprintEncodeData dims=30 metadata=metadata.csv umap_markers_plot=True microbiome_min_cells=1 species=human metadata_column=condition min_features=200 max_molecules=Inf test_use=wilcox min_percentage_to_plot=2 variable_selection_method=vst percent_mt=auto microbiome_min_features=3 percent_rp=0 doublet_filter=T taxa=genus reduction=cca scale_factor=10000 tsne_markers_plot=False celltypist_model=Immune_All_Low.pkl logfc_threshold=0.25 organism=hsa show_labels=T confidence=0.05 min_hit_groups=4 max_features=Inf min_cells=3 normalization_method=LogNormalize resolution=auto highly_variable_features=2000 mapping=org.Hs.eg.db marker_plots_per_cluster_n=20 runid=dbe85684 is_integrated_sample=True option=advanced' returned non-zero exit status 1.
Last few lines from the log file:
[Thu Jul 25 13:07:26 2024]
rule kegg_enrichment:
input: results_integrated/integrated/percent_mt~auto/resolution~auto/table_all-markers-seurat_clusters.xlsx
output: analyses_integrated/kegg/percent_mt~auto/resolution~auto/integrated-seurat_clusters-kegg.rds, results_integrated/integrated/percent_mt~auto/resolution~auto/enrichment_analysis/table_KEGG-enrichment-seurat_clusters.xlsx, results_integrated/integrated/percent_mt~auto/resolution~auto/enrichment_analysis/table_KEGG-geneset_enrichment-seurat_clusters.xlsx, results_integrated/integrated/percent_mt~auto/resolution~auto/enrichment_analysis/table_KEGG-module_enrichment-seurat_clusters.xlsx, results_integrated/integrated/percent_mt~auto/resolution~auto/enrichment_analysis/table_KEGG-module_geneset_enrichment-seurat_clusters.xlsx
jobid: 18
reason: Missing output files: results_integrated/integrated/percent_mt~auto/resolution~auto/enrichment_analysis/table_KEGG-enrichment-seurat_clusters.xlsx, results_integrated/integrated/percent_mt~auto/resolution~auto/enrichment_analysis/table_KEGG-module_geneset_enrichment-seurat_clusters.xlsx, results_integrated/integrated/percent_mt~auto/resolution~auto/enrichment_analysis/table_KEGG-module_enrichment-seurat_clusters.xlsx, results_integrated/integrated/percent_mt~auto/resolution~auto/enrichment_analysis/table_KEGG-geneset_enrichment-seurat_clusters.xlsx; Input files updated by another job: results_integrated/integrated/percent_mt~auto/resolution~auto/table_all-markers-seurat_clusters.xlsx
wildcards: sample=integrated, percent_mt=auto, resolution=auto, i=seurat_clusters
resources: tmpdir=/tmp
[Thu Jul 25 13:07:33 2024]
Finished job 1.
35 of 43 steps (81%) done
[Thu Jul 25 13:08:11 2024]
Finished job 9.
36 of 43 steps (84%) done
[Thu Jul 25 13:09:32 2024]
Finished job 18.
37 of 43 steps (86%) done
[Thu Jul 25 13:24:52 2024]
Finished job 16.
38 of 43 steps (88%) done
[Thu Jul 25 15:13:38 2024]
Finished job 41.
39 of 43 steps (91%) done
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-07-25T092757.755271.snakemake.log
I've found a workaround to the current issue. I did the usual steps (1-3), without supplying the metadata
to cellsnake version 0.2.0.12 and then ran the previous version 0.2.0.11 as step 4 for plotting condition-specific DE markers.
docker run -m 120g --cpus 20 \
--rm -v "$(pwd):/app" sinanugur/cellsnake:0.2.0.12 cellsnake advanced fetal-brain/data \
--configfile config.yaml --jobs 20
[Thu Aug 8 09:18:17 2024] Finished job 0. 53 of 53 steps (100%) done Complete log: .snakemake/log/2024-08-08T085227.509111.snakemake.log Samples detected : S10X_17_029 S10X_17_028
docker run -m 120g --cpus 20 \
--rm -v "$(pwd):/app" sinanugur/cellsnake:0.2.0.12 cellsnake integrate fetal-brain/data --jobs 20
[Thu Aug 8 09:20:17 2024] Finished job 0. 2 of 2 steps (100%) done Complete log: .snakemake/log/2024-08-08T091909.400967.snakemake.log Samples detected : S10X_17_029 S10X_17_028
docker run -m 120g --cpus 20 \
--rm -v "$(pwd):/app" sinanugur/cellsnake:0.2.0.12 cellsnake integrated \
advanced analyses_integrated/seurat/integrated.rds --resolution 0.8 --jobs 20
[Thu Aug 8 10:05:29 2024] Finished job 0. 40 of 40 steps (100%) done Complete log: .snakemake/log/2024-08-08T092038.572432.snakemake.log Samples detected : integrated
docker run -m 120g --cpus 20 \
--rm -v "$(pwd):/app" sinanugur/cellsnake:0.2.0.11 cellsnake integrated \
standard analyses_integrated/seurat/integrated.rds --resolution 0.8 \
--metadata metadata.csv --jobs 20
[Thu Aug 8 10:06:35 2024] Finished job 0. 6 of 6 steps (100%) done Complete log: .snakemake/log/2024-08-08T100618.444608.snakemake.log {'integrated'}
Hi, Thank you so much for the workflow. I'm recently facing the below issue at the DE step. Could you kindly have a look at the issue when possible?
Analyzing fetal-brain test data
download data
S10X_17_028 S10X_17_029
activate cellsnake env
update metadata
sample,condition S10X_17_028,A S10X_17_029,B
successful
failing