staramr error

[kayobianco]

Hello everybody,

I have the following error:

(hamronization_workflow) kayobianco@unixkayo:~/hAMRonization_workflow$ ./run_test.sh Assuming unrestricted shared filesystem usage. host: unixkayo Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --colors to define parallelism) Rules claiming more threads will be scaled down. Job stats: job count

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all 1 get_amrfinder_db 1 hamronize_amrfinderplus 1 hamronize_deeparg 1 hamronize_groot 1 hamronize_resfams 1 hamronize_resfinder 1 hamronize_srst2 1 hamronize_staramr 1 run_amrfinderplus 1 run_deeparg_fqs 1 run_srst2 1 run_staramr 1 summarize_all 1 summarize_sample 1 total 15

Select jobs to execute... Run 1 jobs...

[Tue Feb 18 23:33:59 2025] Job 45: Running rule run_staramr on NDM_biosample with contigs Reason: Missing output files: results/NDM_biosample/staramr/resfinder.tsv, results/NDM_biosample/staramr/metadata.txt

Activating conda environment: .snakemake/conda/2f2d0a08d44ed03ed97ac2ae43fa9fec_ [Tue Feb 18 23:34:03 2025] Error in rule run_staramr: jobid: 45 input: test/simple/test_contig.fna output: results/NDM_biosample/staramr/resfinder.tsv, results/NDM_biosample/staramr/metadata.txt log: logs/staramr_NDM_biosample.log (check log file(s) for error details) conda-env: /home/kayobianco/hAMRonization_workflow/.snakemake/conda/2f2d0a08d44ed03ed97ac2ae43fa9fec_ shell:

rm -r results/NDM_biosample/staramr/; staramr search -o results/NDM_biosample/staramr/ --nproc 1 test/simple/test_contig.fna >logs/staramr_NDM_biosample.log 2>&1 staramr --version | perl -p -e 's/staramr (.+)/--analysis_software_version $1/' > results/NDM_biosample/staramr/metadata.txt grep "resfinder_db_commit" results/NDM_biosample/staramr/settings.txt | perl -p -e 's/.+= (.+)/--reference_database_version $1/' >> results/NDM_biosample/staramr/metadata.txt

(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-02-18T233357.795399.snakemake.log WorkflowError: At least one job did not complete successfully.

Can you help me?

Best regards, Kayo