# GenBank/RefSeq Directory Structure

### Overview of directories

- `$gbRoot/` - root directory
  - `etc/` - configuration files and scripts
    - `ignore.idx` - ignore index file.
    - `genban.conf` - configuration file.
  - `data/` - data files
    - `download/` - downloaded files from NCBI ftp
      - `genbank.${ver}/`
      - `genbank.${ver}/daily-nc/`
      - `refseq.${ver}/cummulative/`
      - `refseq.${ver}/daily/`
    - `processed/` - data extracted from the NCBI flat-files
      - `genbank.${ver}/`
        - `full/`
        - `daily.${date}/`
      - `refseq.${ver}/`
        - `full/`
        - `daily.${date}/`
    - `aligned/` - aligned sequences
      - `${db}/`
    - `var/build/` - files associated with download and build steps. Only on build server
      - `run/` - semaphore files
      - `logs/` - log files
      - `build.time` - File contain the time that the last download and alignment steps completed, in seconds since 00:00:00 1970-01-01 UTC. This is used by process running on other systems to poll for completion.
    - `var/copy/` - files associated with copying to the gbdb server.
      - `run/` - semaphore files
      - `logs/` - log files
      - `build.time` - copy of `build/build.time` from the last completed copy.
      - `copy.time` - file containing time last copy completed.
    - `var/dbload/$host/` - files associated with that last database load on database server $host.
      - `run/` - semaphore files
      - `logs/` - log files
      - `copy.time` - copy of `copy/copy.time` from the last completed copy.
      - `load.time` - file containing time last load completed completed.