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

---

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