Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

D
Appendix D Advanced Topic: Primary Analysis
Procedures to verify primary analysis status
Procedure for re-analyzing the image (primary analysis)
If there was failure in the automatically-generated primary analysis
pipeline, there are two ways to do primary re-analysis of the image.
Before doing so, look at the primary log files to find out reason of
failure. The log files are in the folder:
/data/result/{instrument.name}/{run.name}/{sample.name}/
jobs/{stage.name}.[JobId]/analysis/
Also, ensure that all images are present at /data/images/{run.name}.
After finding out the reason, change primary analysis parameters.
To re-analyze through SETS:
1. Log in to SETS using an administrative account.
2. Modify the primary analysis settings. Either modify added
parameters or add your new values in Additional parameter
field.
3. Open the Run Details page for that run and do primary reanalysis.
To perform primary analysis manually:
1. Access the job folder at:
/data/result/{instrument.name}/{run.name}/{sample.n
ame}/jobs/{stage.name}.[JobId]/
2. Modify the parameters.ini file with the desired value.
3. Enter the following command:
jprimaryanalysis.sh --dir=
--ini=
For example:
jprimaryanalysis.sh
-dir=/data/results/DAEMONAC2/LAST_MP_1245_041008/Sam
ple1/jobs/ postPrimerSetPrimary.3793 -ini=parameters.ini
190 Applied Biosystems SOLiD 4 System SETS Software User Guide