scripts/SLURM_JOBS.md

SLURM Job Scripts

Quick reference for submitting jobs to the cluster.

Available Jobs

Script	Purpose	Resources	Usage
slurm_verify.sh	Verify paper results	32G RAM, 1hr	sbatch scripts/slurm_verify.sh [syn30|fdr|dali|all]
slurm_embed.sh	Embed FASTA sequences	64G RAM, GPU, 4hr	sbatch scripts/slurm_embed.sh input.fasta output.npy
slurm_calibrate_fdr.sh	Compute FDR thresholds	32G RAM, 2hr	sbatch scripts/slurm_calibrate_fdr.sh

Verification Options

• syn30 - JCVI Syn3.0 annotation (Paper Figure 2A: 59/149 = 39.6%)
• fdr - FDR algorithm verification
• dali - DALI prefiltering (Tables 4-6: 82.8% TPR, 31.5% DB reduction)
• clean - CLEAN enzyme classification (Tables 1-2: hierarchical loss control)
• all - Run all verifications

Note: Full CLEAN verification with precision/recall metrics requires the CLEAN package from https://github.com/tttianhao/CLEAN. The basic verification uses pre-computed data.

Quick Commands

# Check job status
squeue -u $USER

# View job output (use Read tool or cat, avoid tail -f on login node)
cat logs/cpr-verify-JOBID.out

# Cancel a job
scancel JOBID

# Submit verification jobs
sbatch scripts/slurm_verify.sh syn30
sbatch scripts/slurm_verify.sh dali
sbatch scripts/slurm_verify.sh all

# Submit other jobs
sbatch scripts/slurm_embed.sh my_sequences.fasta my_embeddings.npy
sbatch scripts/slurm_calibrate_fdr.sh

Output

All jobs write to logs/ directory:

• logs/cpr-JOB-JOBID.out - stdout
• logs/cpr-JOB-JOBID.err - stderr