HELP!

This page provides general strategies for troubleshooting common SMRT^® Analysis issues and offers solutions to previously encountered problems. Articles on this page will help you solve most SMRT Analysis issues.

• SMRT Analysis Install
  • 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
  • qsub command not found
  • OSError: [Errno 13] Permission denied
• SMRT Analysis Upgrade
  • User does not have the correct permissions to upgrade
  • Finding $SEYMOUR_HOME on an existing SMRT Analysis Installation
• SMRT Analysis Log Files
• SMRT Analysis Migration
  • How to migrate SMRT Analysis to a different server

• 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 message
• Creating/Running Jobs
  • SMRT® Portal job fails
  • 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 - mj
  • Job fails at exactly 12 hour - mj
  • 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
• Import and Manage Data
  • Cannot import new SMRT cells
  • Reference upgrades fail
  • Automatic secondary analysis processing does not work
  • How to delete SMRT cells

• 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

• 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