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.