gsReporter Executable

2. GS Reporter : 2.1 gsReporter Executable

2.1	gsReporter Executable

The gsReporter executable generates various human-readable files which can be used to examine the results of a sequencing Run. These include files pertaining to read data, FASTA files (*.fna), associated base quality score files (*.qual), and legacy files (*.wells, etc.). The gsReporter also generates files containing the Run metrics in text (*.txt) and comma-separated value (*.csv) files.

Figure 7: gsReporter section of an XML processing script (options should appear on one line)

The default output files of the gsReporter are specified in the gsReporter section of the signal processing XML pipeline script (Figure 7) and are indicated in the options table below by the shaded rows. The default location of the output files can be redirected to alternate locations, using the --out option of the gsReporter command, or to standard output, using the --console option, for piping of the gsReporter command in a script. The gsReporter will attempt to generate all output files specified even if it does not have the required information. For example, generating a FASTA file on an image-processed only CWF file will result in an empty .fna file and a warning message will be sent to the console.

The gsReporter command line has the following form:

gsReporter [OPTIONS] SOURCE_FILES

Command	Description
gsReporter	An application that extracts read trace information and Run metrics from CWF files to generate various human-readable files, including FASTA files (.fna), associated base quality score files (.qual), legacy files (.wells, etc.; files generated from pre-2.0 software), and Run metrics files in text (.txt) and comma-separated value (*.csv) formats.

Argument	Description
SOURCE_FILES	List of CWF data files to be processed.

Option*	Description
--console	Redirects output to standard output. Used when piping the gsReporter command in a script.
--out	Redirects output to an alternate (non-default) output location By default, the GS Reporter application attempts to write its output files to the locations they would have been placed by earlier versions of the software.
--dump	Dumps all XML in the corrected CWF file as a single document. (binary)
--info	Shows summary information about the CWF file.
--legacy	Simulate the output of a GS Junior or GS FLX+ sequencing Run processed with pre-2.0 software.
-a, --all	Generates all output files.
--fna	Generates one FNA file per library key per region for a corrected CWF file.
--qual	Generates one qual file per library key per region for a corrected CWF file.
--meta	Extracts the meta information about a region’s data as an XML file.
--metrics	Extracts the metrics information about a region’s data as an XML file.
--wells	Generates a .wells file per region.
--cfValues	Generates one cfValues file per region for a corrected CWF file. This is a binary file that contains information about the CAFIE correction data. This file is used by the gsSupportTool for troubleshooting Runs. (Binary)
--454RuntimeMetricsAll.txt	Generates a 454RuntimeMetricsAll.txt file for the Run.
--454RuntimeMetricsAll.csv	Generates a 454RuntimeMetricsAll.csv file for the Run.
--454BaseCallerMetrics.txt	Generates a 454BaseCallerMetrics.txt file for the Run.
--454BaseCallerMetrics.csv	Generates a 454BaseCallerMetrics.csv file for the Run.
--454RuntimeMetrics.txt	Generates one 454RuntimeMetrics.txt per key per region.
--454RuntimeMetrics.csv	Generates one 454RuntimeMetrics.csv per key per region.
--454QualityFilterMetrics.txt	Generates a 454QualityFilterMetrics.txt file for the Run.
--454QualityFilterMetrics.csv	Generates a 454QualityFilterMetrics.csv file for the Run.
--cafieMetrics	Generates one cafieMetrics.csv file per region. (binary)
--droopEstimate	Generates one droopEstimate file per region. (binary)
--trimInfo	Generates one trimInfo file per region.(binary not used)
--xy	Generates one text file containing a list of well locations, per region.
--csv	Generates one file with the flows written out as comma-separated values per region.
--analysisParms.parse	Generates an approximation of a pre-2.0 analysisParms.parse.
--revisedRegions.parse	Generates a single revisedRegions.parse file.

* Shaded rows denote files that gsReporter outputs by default

The binary files are an intermediate product of processing and do not contain metric information. They are used by the pipeline processing job.