GECCO Error

[andrekind17]

Hi Matin, when I run GECCO on the Lactobacillus_delbrueckii example dataset with bgcflow run, I get this error:

/usr/bin/bash: line 2: 657128 Illegal instruction (core dumped) gecco run --genome data/interim/processed-genbank/GCA_000014405.1.gbk --output-dir data/interim/gecco/0.9.10/GCA_000014405.1 --antismash-sideload --jobs 2 --force-tsv 2>> logs/gecco/run/0.9.10_GCA_000014405.1.log

[Wed Sep 25 13:46:48 2024] Error in rule gecco: jobid: 98 input: data/interim/processed-genbank/GCA_000014405.1.gbk output: data/interim/gecco/0.9.10/GCA_000014405.1/GCA_000014405.1.clusters.tsv log: logs/gecco/run/0.9.10_GCA_000014405.1.log (check log file(s) for error details) conda-env: /mnt/data/studenti/agentile/bgcflow/.snakemake/conda/fc38642a72f0d9780c1726281ad2a8f0_ shell:

gecco run --genome data/interim/processed-genbank/GCA_000014405.1.gbk --output-dir data/interim/gecco/0.9.10/GCA_000014405.1 --antismash-sideload --jobs 2 --force-tsv 2>> logs/gecco/run/0.9.10_GCA_000014405.1.log

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

Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-25T134640.083718.snakemake.log WorkflowError: At least one job did not complete successfully. Stopping panoptes server: PID 655760

This is the log file: 2024-09-25T134640.083718.snakemake.log

If I run GECCO with snakemake -s /home/agentile/data/bgcflow/workflow/rules/gecco.smk, I get this specific error:

WorkflowError in file /home/agentile/data/bgcflow/workflow/rules/gecco.smk, line 22: Rule antismash_db_setup is not defined in this workflow. Available rules: gecco

Seems like it's finding problems in the snakefile.