Known Issues

This page lists known issues in the most recent release of CloVR that we are actively working to resolve. If you have trouble with something not listed here, please email us so that we may document and quickly address your issue.


  • Postgres database files are located on the root filesystem which can lead to the VM running out of space and becoming unresponsive in the event of one large or several CloVR Comparative runs.
  • Output data from CloVR pipelines are produced across multiple directories. We are working to consolidate the results from each pipeline into a single concise directory structure.
  • Some error conditions (e.g. running out of disk space or RAM) may cause silent pipeline errors. Pipelines in this case must then be terminated from the command line. (see Troubleshooting page).
  • Pipelines cannot be killed without manually terminating the cluster (vp-terminate-cluster) or clearing the SGE queue using qdel. Read how to kill unresponsive pipelines page for further information.
  • It is not possible to re-run a pipeline twice with identical input datasets and parameters. Either the dataset name or parameters must be adjusted to re-run a pipeline.
  • The master on the cloud will auto shut down once it is left idle for as long as 2 hours. This is implemented in order to prevent further costs to the user if the master is left with out shut down in the cloud, especially on EC2 platform. If user, for any reason, wants to keep the master in the cloud alive even after pipeline completion, please login onto the master in the cloud using SSH and execute the following command: touch /var/vappio/runtime/noautoshutdown


  • DIAG machines intermittently become unresponsive.
  • When internet transfer speeds are too slow (i.e. it takes longer than 2 hours to upload your data to the cloud) the cluster automatically terminates to reduce unnecessary cost. Using a home-based internet connection with ~1MB/sec upload time, this equates to 7+ GB of data can be uploaded in two hours.


  • CloVR-Search will fail when any input data causes the associated BLAST job to fail.


  • BSML output files are not downloaded by default.


  • Mapping files must contain newline characters rather than Windows-based carriage returns (e.g. “\r”, “^M”).


  • Mapping files must contain newline characters rather than Windows-based carriage returns (e.g. “\r”, “^M”).