FAQ for the QPCR web application
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README.md

README.md

QPCRWebApp

FAQ for the QPCR web application. Pubmed

www.icbi.at/qpcr

Installation: Troubleshooting

######JAVA problem######

  • Possible solution: The main sticking point was the location of JRE required by the software. I had to set the path for JAVA_HOME to the location of JRE within the JDK directory because the path ../server/jmv.dll was located there. The other issue was that you had to start the servers an administrator or they wouldn’t work.

######PostgreSQL problem###### When using a PostgreSQL version >9.0 the database needs to be adjusting using this command

ALTER DATABASE database_name SET bytea_output TO 'escape';

See: http://badrit.com/blog/2011/1/19/postgresql-9-bytea-type-problems#.VieYhXVSuko

######Suse problem###### We have experienced problems when installing QPCR on the Suse distribution (probably an issue with the Java installation). If possible, please use another distribution (e.g., Ubuntu).

Installation: Checks

After installation there are a couple of things you could do to check if the system is running properly:

  • Check if both QPCR and the Usermanagement system are up and running
  • Try to log into the Usermanagement System and check if the QPCR account is still valid (Users -> show all -> application status)
  • Check the log files for detailed error messages

Installation: No credentials for databases (Step 7)

Error message: "Could not connect to the specified database"

Step 7 of the installation asks for database credentials (username and password).

Before starting the QPCR installer you need to have a running instance of a Postgresql or Oracle database and create two users (one for the usermanagement system and one for the QPCR system) to access it. In step 7 the username and pwd of these database users are requested.

Hint: check out http://www.postgresql.org/download/windows for a Windows installer.

"Plate has no values to analyse" with LightCycler

For LightCycler users: If you're getting a "Plate has no values to analyse" error message during parsing please make sure that the ‘point index’ check box is checked when exporting the .xml file.

Errors during parsing

File could not be parsed Please make sure that you assign a name for all wells (especially when using Abi SDS). QPCR takes this name as sample name and uses it later in subsequent analysis steps.

File Format not supported - Unexpected length of RAW section The SDS file seems to be corrupted. Please try to save it again and re-upload it into the QPCR application.

Tutorial files appear to corrupted

If you either cannot download the tutorial files or cannot extract the zip file please download the files from tutorialFiles.zip and try it again.

What qPCR machines are supported?

The following qPCR machines are supported by QPCR:

  • ABI 7000 (SDS file, exported component file, exported deltaRn file)
  • ABI 7500 (EDS file, exported file including Sample Setup and Amplification Data)
  • ABI 7900 (SDS file, exported clipped file)
  • LightCycler 2.0 (IXO file, exported Fluorescence history (over Cycles) as XML file)
  • LightCycler 480 (IXO file, exported Fluorescence history (over Cycles) as XML file) For machines that are not supported please use the generic CSV format.