---
title: Batch jobs & exports
description: Run BLAST across many query files in one job and package the results for storage.
---

Run [BLAST](/docs/blast) across many query files in one run and package the results for storage. The concurrency setting (`-P` in the runner) is what most affects throughput — tune it to the vCPUs available so parallel searches don't oversubscribe the machine.

> **Where these commands run**

> You cannot open a shell on the platform yourself. The commands on this page are BLAST+ command lines: ask Ivy in chat to run them in the chat's [code workspace](/docs/sandbox), which ships BLAST+, or run them on your own machine. For a hosted search with no commands, see the [BLAST quickstart](/docs/blast/quickstart).

## Batch runner script (bash)

```bash
#!/usr/bin/env bash
set -euo pipefail

DB="inputs/db/genomes_v1"
OUT_DIR="outputs/batch"
mkdir -p "$OUT_DIR"

find inputs/sequences -name "*.fasta" -print0 | xargs -0 -n1 -P4 -I{} bash -c '
  file="$1"
  base=$(basename "$file" .fasta)
  blastn \
    -query "$file" \
    -db '"'"'$DB'"'"' \
    -out '"'"'$OUT_DIR'"'"'/"$base".tsv \
    -outfmt "6 qseqid sseqid pident length evalue bitscore" \
    -max_target_seqs 5
' _ {}
```

- Adjust `-P4` to control concurrency.
- Emit a per-file TSV to keep failures isolated.

## Capture run metadata

Write a `SUMMARY.json` next to outputs:

```bash
python - <<'PY'
import json, os, subprocess, hashlib

def md5(path: str) -> str:
    h = hashlib.md5()
    with open(path, "rb") as f:
        h.update(f.read())
    return h.hexdigest()

summary = {
    "blast_version": subprocess.check_output(["blastn", "-version"], text=True).strip(),
    "database": "inputs/db/genomes_v1",
    "database_checksums": [md5(p) for p in sorted(os.listdir("inputs/db")) if p.startswith("genomes_v1")],
    "outputs": sorted(os.listdir("outputs/batch")),
}

with open("outputs/batch/SUMMARY.json", "w", encoding="utf-8") as handle:
    json.dump(summary, handle, indent=2)
PY
```

## Export results for S3

```bash
tar -czf outputs/blast_results.tar.gz -C outputs/batch .
```

Upload the tarball; keep `SUMMARY.json` to describe the run.