Spaces:
Running
Running
File size: 1,601 Bytes
3f702bf | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | # 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
```bash
# 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
|