Error in rule generate_results_summary for test dataset #43
Description
Hi,
I am trying to use kGWASflow on the test dataset (100 individuals) before using on my data, and I noticed that when the pipeline was almost done (610 of 612 steps (99.7%) done), it failed at the rule generate_results_summary:
Error in rule generate_results_summary:
jobid: 611
input: results/kmers_gwas/disease/kmers/pass_threshold_5per
output: results/tables/kmers_gwas_summary/disease/kmers_gwas.results_summary.5per.txt, results/tables/kmers_gwas_summary/disease/kmers_gwas.results_summary.10per.txt, results/plots/pval_hist/disease, results/tables/kmers_gwas_summary/disease/generate_results_summary.done
log: logs/tables/kmers_gwas_summary/disease/generate_kmers_gwas_results_summary.log (check log file(s) for error details)
conda-env: /nfs7/BPP/LeBoldus_Lab/zaccaroa/test3/.snakemake/conda/4dd7e37e77255b7d4473475a58a9a94f_
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-02-07T124453.728212.snakemake.log
ERROR:root:Error running Snakemake: Command '['snakemake', '--use-conda', '--conda-frontend', 'conda', '--cores', '16', '--snakefile', '/nfs7/BPP/Weisberg_Lab/lab_members/zaccaron/miniforge3/envs/kgwasflow/lib/python3.11/site-packages/workflow/Snakefile', '--rerun-triggers', 'mtime', 'params', 'input', 'software-env', 'code']' returned non-zero exit status 1.
The input file results/kmers_gwas/disease/kmers/pass_threshold_5per is empty
The log file logs/tables/kmers_gwas_summary/disease/generate_kmers_gwas_results_summary.log is empty.
Here's the content of results/:
kmers_count/
kmers_gwas/
kmers_list/
kmers_table/
plots/
qc/
reads/
tables/
and results/kmers_gwas/disease/kmers/output/ was empty.
Details:
- Using SLURM HPC Rocky Linux 9.5 (Blue Onyx)
- Installed via bioconda
- Before running kGWASflow, I fixed the test reads to remove reads with empty sequences and singletons
All steps I performed to install and run kGWASflow can be replicated, as described here kGWASflow_install_notes.md.txt
I really appreciate any insight to solve the issue.
Thanks,
Alex