Troubleshooting the SMRT Analysis Suite - dyim42/SMRT-Analysis GitHub Wiki

This troubleshooting guide provides general strategies for troubleshooting SMRT Analysis issues and offers solutions to common problems.

##Technical Support Tools## When getting support from Pacific Biosciences, you may be asked to install and run some technical support tools. See the links below for instructions.

• Installing and upgrading the techsupport tools
• Using the techsupport tools

##SMRT Analysis Installation##

• Installation
  • The configure_smrtanalysis.sh script fails
  • Cannot create a mysql database
  • Installation assumes local MySQL instance
  • Environment variables are not set correctly
  • Cannot create softlinks to services
• Upgrade
  • User does not have the correct permissions to upgrade
  • Finding $SEYMOUR_HOME on an existing SMRT Analysis Installation
• SMRT Analysis Migration
  • How to migrate SMRT Analysis to a different server
• SMRT Analysis Uninstalls
  • How to uninstall SMRT Analysis
• Locating SMRT Analysis Log Files

##SMRT Portal##

• Administration
  • Cannot See The SMRT Portal Page
  • You can start SMRT Portal, but cannot log in
  • Cannot register administrator for the first time due to hibernate.dialect error
  • SMRT Portal Lost administrator password
  • SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder"
• Creating/Running Jobs
  • SMRT Portal job fails
  • Common SMRT Portal Errors
  • RS HGAP Assembly protocol fails in SMRT Portal
  • smrtpipe.log Error: java.lang.OutOfMemoryError: Java heap space
  • SMRT Portal has dificulty connecting to the smrtportal mysql database
  • SMRT Portal freezes
  • SMRT Portal job status does not update
  • SMRT Portal GMAP "No such file or directory" error
  • KeyError: "unable to open object (Symbol table: Can't open object)"
• Distributed Computing
  • The job is very slow
  • SMRT Portal jobs are being submitted as root
  • Job fails at exactly 12 hour
  • When using the sync option in SGE, you may see errors
  • The head node is very slow when more than 20 jobs are running
  • Head node may run out of resources
  • qsub: command not found
• Import and Manage Data
  • Cannot import new SMRT Cells
  • Reference upgrades fail
  • Troubleshooting Kodos Secondary Auto Analysis
  • Delete SMRT Cells from SMRT Portal
• Known System Issues
  • SMRT View runs out of resources

SMRT View

• Common Problems
  • SMRT View does not launch
  • SMRT View is slow
  • SMRT View is downloaded from the server every time you access it
  • SMRT View does not show reads in the details panel
  • SMRT View crashes while browsing
  • SMRT View security certificate warning message
• Alternate Configurations
  • Running SMRT View in a different tomcat instance

Celera® Assembler

• Stopping Celera Assembler jobs
• Job fails if a soft link resolves to 2 different paths
• Timing problem with jobs
• Celera Assembler deadlocks in distributed mode
• Customizing a spec file using a setting not exposed in the UI
• Default parameters are set conservatively