HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017Simultaneously run RNA-Seq jobs using the EM option can fail or produce incorrect results on Workbenches

3.4. Simultaneously run RNA-Seq jobs using the EM option can fail or produce incorrect results on Workbenches

The issue described below has been fixed for CLC Genomics Workbench 9.5.2 and Biomedical Genomics Workbench 3.5.2. If you are running the CLC Genomics Workbench 9.5.1 or 9.5, Biomedical Genomics Workbench 3.5.1 or 3.5, please update your installation.

 

Issue description

Using CLC Genomics Workbench 9.5.1 and 9.5 and Biomedical Genomics Workbench 3.5.1 and 3.5, RNA-Seq Analysis may fail or report wrong results if multiple instances of the RNA-Seq Analysis tool are run simultaneously with the EM option turned on.

The following conditions are necessary before the issue can arise:

  • RNA-Seq Analysis is run with the EM option turned on AND
  • Two or more such RNA-Seq Analysis tasks are run concurrently.

This does not affect jobs run using the Batch option, or jobs run on a CLC Genomics Server.

 

Actions to take

Upgrade your Workbench to the latest version.

We generally recommend generally that the Batch option is used for launching multiple instances of a particular type of analysis. Using this option, jobs launched are run sequentially.

If you have been running multiple RNA-Seq analyses simultaneously on an affected Workbench, and you are not able to upgrade immediately, then on your current Workbench, re-run the RNA-Seq Analysis tasks sequentially.

Symptoms of this issue

One or more of the concurrently run RNA-Seq Analysis tasks fails with an error. Currently we are aware of three possible error messages being associated with this issue: "Index out of bounds", IllegalArgumentException" and "Modifying call after finished not supported".

Some concurrently run RNA-Seq Analysis tasks that have EM turned on may succeed, but these may include incorrect results.

 

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