Move digger reproduction env to tools/reproduction/

- Moved bttoxin_digger_v5_repro to tools/reproduction/bttoxin_digger
- Updated docker-compose.yml to point to the new location
- This declutters the root directory while preserving the reproduction environment

tools/reproduction/bttoxin_digger/AGENTS.md

@@ -0,0 +1,206 @@
+# BtToxin_Digger v5 Reproduction - AGENTS.md
+
+本文档为 AI 助手和开发者提供 bttoxin_digger_v5_repro 项目的快速参考指南。
+
+## 项目概述
+
+BtToxin_Digger v5 Reproduction 是一个基于 Pixi 和 Docker 的 BtToxin_Digger 1.0.10 可复现运行环境，集成了最新的 BLAST v5 毒素数据库。
+
+**核心功能：**
+- 使用 `ghcr.io/prefix-dev/pixi:latest` 作为基础镜像
+- 预装 BtToxin_Digger 1.0.10 和 BLAST+ 2.16.0
+- 内置最新版本的 BtToxin 数据库（20251104）
+- 支持 Docker 容器化部署
+
+## 目录结构
+
+```
+bttoxin_digger_v5_repro/
+├── docker/
+│   └── Dockerfile              # Docker 镜像构建文件
+├── docker-compose.yml          # 本地测试编排配置
+├── external_dbs/               # 外部数据库源（构建时复制到镜像）
+│   └── bt_toxin/
+│       ├── db/                 # BLAST 索引文件 (.phr, .pin, .psq)
+│       │   ├── bt_toxin.pdb    # 数据库元数据
+│       │   ├── bt_toxin.phr    # 蛋白质序列头索引
+│       │   ├── bt_toxin.pin    # 蛋白质序列索引
+│       │   ├── bt_toxin.psq    # 蛋白质序列数据
+│       │   └── old/            # 历史索引备份
+│       └── seq/                # FASTA 序列源文件
+│           ├── bt_toxin20251104.fas  # 最新毒素序列（2025年11月）
+│           ├── bt_toxin20221208.fas
+│           └── updateDB.py            # 数据库辅助脚本
+├── pixi.toml                   # Pixi 环境依赖定义
+├── pixi.lock                   # 依赖版本锁定文件
+├── examples/                   # 测试用例
+│   └── inputs/                 # 输入文件
+│       └── C15.fna             # 测试基因组文件
+└── README.md                   # 项目说明文档
+```
+
+## 快速开始
+
+### 构建 Docker 镜像
+
+```bash
+cd bttoxin_digger_v5_repro
+docker compose build
+```
+
+### 运行分析（本地测试）
+
+```bash
+# 查看帮助
+docker compose run --rm digger-repro pixi run BtToxin_Digger --help
+
+# 运行分析
+docker compose run --rm digger-repro pixi run BtToxin_Digger \
+  --SeqPath /app/jobs \
+  --Scaf_suffix .fna \
+  --threads 4
+```
+
+### 使用主服务中的 Digger 容器
+
+主项目的 `docker/docker-compose.yml` 中包含一个持久运行的 `digger` 服务：
+
+```bash
+# 检查服务状态
+docker ps | grep bttoxin_digger
+
+# 执行分析任务
+docker exec bttoxin_digger pixi run BtToxin_Digger \
+  --SeqPath /data \
+  --Scaf_suffix .fna \
+  --threads 4
+```
+
+## 数据库管理
+
+### 数据库结构说明
+
+- **`seq/` 目录**：存放原始 FASTA 序列文件（如 `bt_toxin20251104.fas`）
+- **`db/` 目录**：存放 BLAST 生成的二进制索引文件
+- **对应关系**：`db/` 中的文件由 `makeblastdb` 命令从 `seq/` 中的 FASTA 文件生成
+
+### 验证数据库版本
+
+```bash
+docker exec bttoxin_digger pixi run blastdbcmd \
+  -db /app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin/db/bt_toxin \
+  -info
+```
+
+**预期输出：**
+```text
+Database: bt_toxin20251104.fas
+Date: Nov 4, 2025  3:35 PM
+BLASTDB Version: 5
+```
+
+### 更新数据库（未来版本）
+
+当上游仓库发布新版本（如 2026/2027 年）时：
+
+```bash
+# 1. 下载新序列文件到 seq/ 目录
+cp /path/to/new/bt_toxin20xxxxxx.fas external_dbs/bt_toxin/seq/
+
+# 2. 重新生成索引（使用 makeblastdb）
+makeblastdb \
+  -in external_dbs/bt_toxin/seq/bt_toxin20xxxxxx.fas \
+  -dbtype prot \
+  -out external_dbs/bt_toxin/db/bt_toxin \
+  -parse_seqids
+
+# 3. 重新构建 Docker 镜像
+docker compose build --no-cache
+
+# 4. 重启服务
+docker compose -f ../docker/docker-compose.yml up -d digger
+```
+
+## 常见任务
+
+### 查看 Digger 帮助
+
+```bash
+docker exec bttoxin_digger pixi run BtToxin_Digger --help
+```
+
+### 重新构建镜像（无缓存）
+
+```bash
+cd bttoxin_digger_v5_repro
+docker compose build --no-cache
+```
+
+### 查看容器日志
+
+```bash
+docker logs bttoxin_digger
+```
+
+### 进入容器交互模式
+
+```bash
+docker exec -it bttoxin_digger pixi run bash
+```
+
+## 故障排查
+
+### 问题：数据库版本不正确
+
+**症状**：分析结果显示使用的是旧版本数据库。
+
+**排查步骤：**
+1. 检查 `external_dbs/bt_toxin/seq/` 目录下的文件是否为最新
+2. 确认 `external_dbs/bt_toxin/db/` 目录下的索引文件与 seq 文件匹配
+3. 验证镜像已重建：`docker images | grep digger`
+4. 重启服务：`docker compose -f ../docker/docker-compose.yml up -d digger`
+
+### 问题：Perl 警告
+
+**症状**：`Possible precedence issue with control flow operator`
+
+**说明**：这是 Perl 5.26 与旧代码的兼容性问题，不影响程序运行，可忽略。
+
+### 问题：容器启动失败
+
+**排查步骤：**
+1. 检查 Docker 是否运行
+2. 查看详细日志：`docker compose logs`
+3. 确认端口未被占用
+
+## 开发说明
+
+### 修改 Dockerfile
+
+如需修改环境依赖：
+1. 编辑 `pixi.toml`（添加/删除依赖）
+2. 运行 `pixi lock` 更新 `pixi.lock`
+3. 重新构建镜像
+
+### 本地开发模式（不使用 Docker）
+
+```bash
+# 安装 Pixi 环境
+cd bttoxin_digger_v5_repro
+pixi install
+
+# 链接外部数据库
+ENV_BIN=.pixi/envs/default/bin
+rm -rf "$ENV_BIN/BTTCMP_db/bt_toxin"
+ln -sfn $(pwd)/external_dbs/bt_toxin "$ENV_BIN/BTTCMP_db/bt_toxin"
+
+# 运行
+pixi run BtToxin_Digger --help
+```
+
+## 相关文件
+
+- `README.md`：项目完整说明（英文）
+- `README_CN.md`：项目完整说明（中文）
+- `docker/Dockerfile`：Docker 镜像构建配置
+- `docker-compose.yml`：本地测试编排配置

tools/reproduction/bttoxin_digger/README.md

@@ -0,0 +1,141 @@
+# BtToxin_Digger (pixi) reproduction & Docker Image
+
+This repo is a **reproducible runtime environment** for BtToxin_Digger 1.0.10, packaged as a Docker image based on `ghcr.io/prefix-dev/pixi`.
+
+It includes:
+1.  **BtToxin_Digger 1.0.10** (installed via Pixi)
+2.  **BLAST+ 2.16.0** (compatible with v5 databases)
+3.  **Pre-bundled BtToxin Database** (baked into the image)
+
+## License / Citation / Disclaimer
+
+- **BtToxin_Digger** is developed by its original authors; cite the upstream publication if you use it in research.
+- **This repository** only provides an environment wrapper (pixi/docker); it does not modify BtToxin_Digger source code.
+
+## 1. Quick Start with Docker
+
+The easiest way to run this is using the included `docker-compose.yml` or the global project configuration.
+
+### Build the Image
+
+```bash
+# In this directory
+docker compose build
+```
+
+### Run Analysis
+
+Place your input `.fna` files in `examples/inputs` (or mount your own directory), then run:
+
+```bash
+# Run help
+docker compose run --rm digger-repro pixi run BtToxin_Digger --help
+
+# Run analysis on a specific file
+# Note: Input path must match the internal mount point (/app/jobs)
+docker compose run --rm digger-repro pixi run BtToxin_Digger \
+  --SeqPath /app/jobs \
+  --Scaf_suffix .fna \
+  --threads 4
+```
+
+### Directory Mounting
+
+- `/app/jobs`: Mount your input sequence files here.
+- `/app/data`: Mount your desired output directory here (if using absolute paths in arguments).
+
+## 2. Docker Image Construction
+
+The image is built using `docker/Dockerfile`.
+
+### Base Image
+Uses `ghcr.io/prefix-dev/pixi:latest` to ensure a consistent conda-compatible environment.
+
+### Database Integration
+The external database (`external_dbs/bt_toxin`) is **copied into the image** during build time.
+Target location: `/app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin`
+
+This replaces the default database shipped with the bioconda package, ensuring:
+1.  Latest toxin definitions are used.
+2.  BLAST v5 indices are compatible with the installed BLAST+ 2.16.0.
+
+### Environment Definition (`pixi.toml`)
+- `bttoxin_digger = "==1.0.10"`
+- `perl = "==5.26.2"` (Legacy requirement)
+- `blast = "==2.16.0"` (Upgraded for v5 DB support)
+- `channel-priority = "disabled"`
+
+## 3. Development / Manual Usage
+
+If you want to run without Docker using local Pixi:
+
+```bash
+# Install environment
+pixi install
+
+# Link the database (required manually if not using Docker)
+# The Dockerfile does this automatically by copying files.
+ENV_BIN=.pixi/envs/default/bin
+rm -rf "$ENV_BIN/BTTCMP_db/bt_toxin"
+ln -sfn $(pwd)/external_dbs/bt_toxin "$ENV_BIN/BTTCMP_db/bt_toxin"
+
+# Run
+pixi run BtToxin_Digger --help
+```
+
+## 4. Repository Layout
+
+```
+.
+├── docker/
+│   └── Dockerfile          # Docker build definition
+├── docker-compose.yml      # Local test orchestration
+├── external_dbs/           # Database source (copied into image)
+│   └── bt_toxin/           # The actual database files
+├── pixi.toml               # Environment dependencies
+├── pixi.lock               # Exact version lock
+└── examples/               # Test inputs and outputs
+```
+
+## 5. Updating the Database (Important for Future Updates)
+
+The database consists of two parts in `external_dbs/bt_toxin`:
+1.  **`seq/` Directory**: Contains the raw FASTA sequence files (e.g., `bt_toxin20251104.fas`).
+2.  **`db/` Directory**: Contains the BLAST indices (`.phr`, `.pin`, `.psq`) generated from the sequences.
+
+**Relationship**: The files in `db/` are **generated from** the FASTA files in `seq/` using `makeblastdb`. The filename of the source FASTA (e.g., `bt_toxin20251104.fas`) is embedded in the `db` files metadata.
+
+### How to Update (e.g., for 2026/2027 data)
+
+If a new database version is released (e.g., from https://github.com/liaochenlanruo/BtToxin_Digger), follow these steps:
+
+1.  **Download New Sequences**:
+    Place the new FASTA file (e.g., `bt_toxin2026xxxx.fas`) into `external_dbs/bt_toxin/seq/`.
+
+2.  **Generate New Indices (Critical Step)**:
+    You must regenerate the indices in `external_dbs/bt_toxin/db/`. You can use a temporary container or local BLAST+ to do this.
+
+    ```bash
+    # Example using the local pixi environment (if installed)
+    # Or use a container with blast installed
+    makeblastdb \
+        -in external_dbs/bt_toxin/seq/bt_toxin2026xxxx.fas \
+        -dbtype prot \
+        -out external_dbs/bt_toxin/db/bt_toxin \
+        -parse_seqids
+    ```
+
+    *Note: The `-out` parameter must end with `bt_toxin` to match what the tool expects.*
+
+3.  **Rebuild Docker Image**:
+    The Dockerfile copies `external_dbs/bt_toxin` into the image. You must rebuild it to include the changes.
+
+    ```bash
+    docker compose build --no-cache
+    ```
+
+4.  **Verify**:
+    Check the database version inside the new container:
+    ```bash
+    docker compose run --rm digger-repro pixi run blastdbcmd -db /app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin/db/bt_toxin -info
+    ```

tools/reproduction/bttoxin_digger/README_CN.md

@@ -0,0 +1,107 @@
+# BtToxin_Digger (pixi) 复现与 Docker 镜像
+
+本仓库提供了一个 **可复现的运行环境**，用于运行 BtToxin_Digger 1.0.10，并打包为基于 `ghcr.io/prefix-dev/pixi` 的 Docker 镜像。
+
+包含内容：
+1.  **BtToxin_Digger 1.0.10** (通过 Pixi 安装)
+2.  **BLAST+ 2.16.0** (兼容 v5 数据库)
+3.  **预置 BtToxin 数据库** (已集成到镜像中)
+
+## 许可证 / 引用 / 免责声明
+
+- **BtToxin_Digger** 由原作者开发；如果在研究中使用，请引用上游发表的论文。
+- **本仓库** 仅提供环境封装 (pixi/docker)；不修改 BtToxin_Digger 源代码。
+
+## 1. 快速开始 (使用 Docker)
+
+最简单的运行方式是使用包含的 `docker-compose.yml` 或全局项目配置。
+
+### 构建镜像
+
+```bash
+# 在本目录下
+docker compose build
+```
+
+### 运行分析
+
+将你的输入 `.fna` 文件放入 `examples/inputs` (或挂载你自己的目录)，然后运行：
+
+```bash
+# 查看帮助
+docker compose run --rm digger-repro pixi run BtToxin_Digger --help
+
+# 对特定文件运行分析
+# 注意：输入路径必须匹配内部挂载点 (/app/jobs)
+docker compose run --rm digger-repro pixi run BtToxin_Digger \
+  --SeqPath /app/jobs \
+  --Scaf_suffix .fna \
+  --threads 4
+```
+
+### 目录挂载说明
+
+- `/app/jobs`: 挂载你的输入序列文件目录。
+- `/app/data`: 挂载你期望的输出目录 (如果在参数中使用绝对路径)。
+
+## 2. Docker 镜像构建原理
+
+镜像使用 `docker/Dockerfile` 构建。
+
+### 基础镜像
+使用 `ghcr.io/prefix-dev/pixi:latest` 以确保一致的 conda 兼容环境。
+
+### 数据库集成
+外部数据库 (`external_dbs/bt_toxin`) 在构建时 **被复制到镜像中**。
+目标位置：`/app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin`
+
+这替换了 bioconda 包自带的默认数据库，确保：
+1.  使用最新的毒素定义。
+2.  BLAST v5 索引与安装的 BLAST+ 2.16.0 兼容。
+
+### 环境定义 (`pixi.toml`)
+- `bttoxin_digger = "==1.0.10"`
+- `perl = "==5.26.2"` (旧版兼容需求)
+- `blast = "==2.16.0"` (升级以支持 v5 数据库)
+- `channel-priority = "disabled"`
+
+## 3. 开发 / 手动使用
+
+如果你想在不使用 Docker 的情况下使用本地 Pixi 运行：
+
+```bash
+# 安装环境
+pixi install
+
+# 链接数据库 (如果不使用 Docker，需要手动操作)
+# Dockerfile 会通过复制文件自动完成此步骤。
+ENV_BIN=.pixi/envs/default/bin
+rm -rf "$ENV_BIN/BTTCMP_db/bt_toxin"
+ln -sfn $(pwd)/external_dbs/bt_toxin "$ENV_BIN/BTTCMP_db/bt_toxin"
+
+# 运行
+pixi run BtToxin_Digger --help
+```
+
+## 4. 仓库结构
+
+```
+.
+├── docker/
+│   └── Dockerfile          # Docker 构建定义
+├── docker-compose.yml      # 本地测试编排
+├── external_dbs/           # 数据库源 (构建时复制到镜像)
+│   └── bt_toxin/           # 实际的数据库文件
+├── pixi.toml               # 环境依赖定义
+├── pixi.lock               # 确切的版本锁定
+└── examples/               # 测试输入和输出
+```
+
+## 5. 更新数据库
+
+要更新容器使用的数据库：
+1. 更新 `external_dbs/bt_toxin/` 中的文件。
+2. 重新构建 Docker 镜像：
+   ```bash
+   docker compose build --no-cache
+   ```

tools/reproduction/bttoxin_digger/docker-compose.yml

@@ -0,0 +1,12 @@
+services:
+  digger-repro:
+    build:
+      context: .
+      dockerfile: docker/Dockerfile
+    image: bttoxin-digger:v5-repro
+    volumes:
+      - ./examples/inputs:/app/jobs
+      - ./examples:/app/examples
+    # Mount the current directory to verify outputs easily if needed
+    # But the DB is now baked in, so no need to mount external_dbs
+    command: pixi run BtToxin_Digger --help

tools/reproduction/bttoxin_digger/docker/Dockerfile

@@ -0,0 +1,28 @@
+# BtToxin Digger v5 容器镜像
+# 基于 pixi 管理的 conda 环境
+
+FROM ghcr.io/prefix-dev/pixi:latest
+
+WORKDIR /app
+
+# 复制 pixi 配置
+COPY pixi.toml .
+COPY pixi.lock .
+
+# 安装依赖
+RUN pixi install
+
+# 复制外部数据库替换默认数据库
+# 注意：必须在 pixi install 之后执行，且需要先清理原有目录以确保完全替换
+# 这一步假设构建上下文包含 external_dbs 目录
+RUN rm -rf /app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin
+COPY external_dbs/bt_toxin /app/.pixi/envs/default/bin/BTTCMP_db/bt_toxin
+
+# 创建工作目录
+RUN mkdir -p /app/jobs /app/data
+
+# 暴露常用端口
+EXPOSE 9000
+
+# 默认命令
+CMD ["pixi", "run", "BtToxin_Digger", "--help"]

tools/reproduction/bttoxin_digger/examples/COMPARE_REPORT.md

@@ -0,0 +1,41 @@
+# BtToxin_Digger pixi vs docker comparison (examples)
+
+## Inputs
+
+- Pixi C15: `runs/bttoxin_digger_v5_repro/examples/C15_pixi_v5/Results/Toxins/All_Toxins.txt`
+- Docker C15: `runs/bttoxin_digger_v5_repro/examples/C15_docker/digger/Results/Toxins/All_Toxins.txt`
+- Pixi HAN055: `runs/bttoxin_digger_v5_repro/examples/HAN055_pixi_v5_clean/Results/Toxins/All_Toxins.txt`
+- Docker HAN055: `runs/bttoxin_digger_v5_repro/examples/HAN055_docker/digger/Results/Toxins/All_Toxins.txt`
+
+Diff files:
+
+- `runs/bttoxin_digger_v5_repro/examples/diffs/C15_docker_vs_pixi_v5.diff`
+- `runs/bttoxin_digger_v5_repro/examples/diffs/HAN055_docker_vs_pixi_v5_clean.diff`
+
+## C15 (docker vs pixi v5)
+
+- Row counts: 24 vs 24
+- Hit_id set: identical
+- Differences: 6 rows differ (4 BLAST E-values, 2 SVM flags)
+
+```
+Protein_id          Field            docker_value  pixi_value
+NZ_CP021436.1_06204 Evalue of blast  1e-35         2e-35
+NZ_CP021436.1_06727 Evalue of blast  9e-33         1e-32
+NZ_CP021436.1_12182 Evalue of blast  7e-60         8e-60
+NZ_CP021438.1_00072 SVM              NO            YES
+NZ_CP021438.1_00163 Evalue of blast  3e-52         4e-52
+NZ_CP021439.1_00043 SVM              YES           NO
+```
+
+## HAN055 (docker vs pixi v5 clean)
+
+- Row counts: 24 vs 24
+- Hit_id set: identical
+- Differences: two rows differ only in the SVM flag
+
+```
+Protein_id        Hit_id    docker_SVM  pixi_SVM
+CP001910.1_00155  Cry2Aa22  YES         NO
+CP001910.1_00475  Cry1Aa3   NO          YES
+```

tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/db/bt_toxin.pjs

@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "bt_toxin",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "bt_toxin20251104.fas",
+  "number-of-letters": 996368,
+  "number-of-sequences": 1199,
+  "last-updated": "2025-11-04T15:35:00",
+  "number-of-volumes": 1,
+  "bytes-total": 1149077,
+  "bytes-to-cache": 1007264,
+  "files": [
+    "bt_toxin.pdb",
+    "bt_toxin.phr",
+    "bt_toxin.pin",
+    "bt_toxin.pot",
+    "bt_toxin.psq",
+    "bt_toxin.ptf",
+    "bt_toxin.pto"
+  ]
+}

tools/reproduction/bttoxin_digger/external_dbs/bt_toxin/seq/updateDB.py

@@ -0,0 +1,36 @@
+def get_unique_headers(file_path):
+    """读取文件中以'>'开头的行，返回'>'后面内容的集合"""
+    headers = set()
+    with open(file_path, 'r') as f:
+        for line in f:
+            line = line.strip()
+            if line.startswith('>'):
+                # 提取'>'后面的内容（包括可能的空格和其他字符）
+                header = line[1:]
+                headers.add(header)
+    return headers
+
+# 输入文件路径
+file1 = 'bt_toxin20251104.fas'
+file2 = 'all_app_cry_cyt_gpp_mcf_mpf_mpp_mtx_pra_prb_spp_tpp_txp_vip_vpa_vpb_xpp_fasta_sequences.txt'
+output_file = 'unique_headers.txt'
+
+# 获取两个文件中的header集合
+headers1 = get_unique_headers(file1)
+headers2 = get_unique_headers(file2)
+
+# 计算各自独有的header
+unique_to_file1 = headers1 - headers2
+unique_to_file2 = headers2 - headers1
+
+# 写入输出文件
+with open(output_file, 'w') as out_f:
+    out_f.write(f"### Unique headers in {file1} ###\n")
+    for header in sorted(unique_to_file1):
+        out_f.write(f">{header}\n")
+    
+    out_f.write(f"\n### Unique headers in {file2} ###\n")
+    for header in sorted(unique_to_file2):
+        out_f.write(f">{header}\n")
+
+print(f"处理完成，结果已保存至 {output_file}")

tools/reproduction/bttoxin_digger/pixi.toml

@@ -0,0 +1,13 @@
+[workspace]
+name = "bttoxin_digger_v5_repro"
+channels = ["bioconda", "conda-forge", "bioconda/label/cf201901"]
+platforms = ["linux-64"]
+version = "0.1.0"
+channel-priority = "disabled"
+
+[dependencies]
+bttoxin_digger = "==1.0.10"
+perl = "==5.26.2"
+perl-file-tee = "==0.07"
+perl-list-util = "==1.38"
+blast = "==2.16.0"

tools/reproduction/bttoxin_digger/run_digger_pixi.sh

@@ -0,0 +1,30 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ $# -lt 2 ]]; then
+  echo "Usage: $0 <input_dir> <scaf_suffix> [threads] [bttoxin_db_dir]"
+  echo "Example: $0 /home/zly/project/bttoxin-pipeline/tests/test_data .fna 4"
+  echo "Example with external DB: $0 /home/zly/project/bttoxin-pipeline/tests/test_data .fna 4 /home/zly/project/bttoxin-pipeline/external_dbs/bt_toxin"
+  exit 1
+fi
+
+input_dir="$1"
+scaf_suffix="$2"
+threads="${3:-4}"
+bttoxin_db_dir="${4:-}"
+
+cache_dir="$(pwd)/.rattler-cache"
+mkdir -p "$cache_dir"
+if [[ -n "$bttoxin_db_dir" ]]; then
+  if [[ -d "$bttoxin_db_dir" ]]; then
+    env_bin="$(RATTLER_CACHE_DIR="$cache_dir" pixi run which BtToxin_Digger | xargs dirname)"
+    ln -sfn "$bttoxin_db_dir" "$env_bin/BTTCMP_db/bt_toxin"
+  else
+    echo "[warn] bttoxin_db_dir not found: $bttoxin_db_dir" >&2
+  fi
+fi
+RATTLER_CACHE_DIR="$cache_dir" pixi run BtToxin_Digger \
+  --SeqPath "$input_dir" \
+  --SequenceType nucl \
+  --Scaf_suffix "$scaf_suffix" \
+  --threads "$threads"