Data Acquisition (GS Sequencer and GS Junior Sequencer) Results: the Run Folder

1. Overview of the 454 Sequencing System Software : 1.3 Data Output and Folder Structure : 1.3.1 Data Acquisition (GS Sequencer and GS Junior Sequencer) Results: the Run Folder

1.3.1

The organization of a generic Run folder (‘R_’) is depicted in Figure 2. All the raw data (raw images, log files, etc.) remain in temporary local storage on the GS FLX+ Instrument or the GS Junior Attendant PC in case the user chooses to re-analyze them (e.g. using the reanalysis function of the GS Run Browser; see Part B, Section 3 of this manual). In addition, if “Backup” is selected during Run set up, raw and processed data files from the Run can be transferred to a network location specified by the System Administrator, for long-term storage.

   R_yyyy_mm_dd_hh_min_sec_machineName_userName_uniqueRunName/
      dataRunParams.parse
      imageLog.parse
      PTP_flowOrder_cycleCount.icl
      runlog.parse
      rawImages/
         00001.png
         00002.png
         00003.png
         …

Figure 2: General organization of a “Run” folder. On the GS FLX+ Instrument or the GS Junior Attendant PC, this is located inside /data/date; while on a DataRig it can be placed anywhere. Words in italics are generic.

Several other files or directories may appear in the R_ directory, which are created for internal use of the software. They are not described in this manual and may indeed be reorganized or eliminated in further releases of the software; they may include the following:

•	Additional files:

◦

aaLog

◦	fpgaReadWriteLog.bin

◦	flowCalibrtionLog.nfc

◦	tempControlLog.ntc

◦

dmesg.txt

◦	debugMessageLog.txt

•	Additional directories:

◦

calibrate

◦

prime

◦

prewash