Page Index - pb-dyim/SMRT-Analysis GitHub Wiki

153 page(s) in this GitHub Wiki:

• Home
• Automatic secondary analysis processing does not work
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• Cannot create a mysql database
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• Cannot create softlinks to services
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• Cannot import new SMRT Cells
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• Cannot register administrator for the first time due to hibernate.dialect error
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• Cannot see the SMRT® Portal page
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• Celera Assembler deadlocks in distributed mode
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• Command line options
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• Customizing a spec file using a setting not exposed in the UI
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• Default parameters are set conservatively
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• Environment variables are not set correctly
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• Finding $SEYMOUR_HOME on an existing SMRT Analysis Installation
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• Head node may run out of resources
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• How to delete smrt cells
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• How to migrate smrt analysis to a different server
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• Installation
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• Installation and Upgrade Summary
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• Installation assumes local mysql instance
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• Instrument Control Web Services API
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• Introduction
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• Issue: when you try to access SMRT View, the application is downloaded from the server
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• Job fails at exactly 12 hour
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• Job fails if a soft link resolves to 2 different paths
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• KeyError: "unable to open object (Symbol table: Can't open object)"
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• Log File Locations
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• Official Documentation
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• Oserror: [errno 13] permission denied
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• qsub command not found
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• Reference upgrades fail
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• Secondary Analysis Web Services API v2.0
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• Slf4j failed to load class org.slf4j.impl.staticloggerbinder message
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• SMRT Analysis Release Notes v2.0
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• SMRT Analysis Software Installation v1.4.0
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• SMRT Analysis Software Installation v2.0
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• SMRT Pipe file structure
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• SMRT Pipe modules and their parameters
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• SMRT Pipe Reference Guide v2.0
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• SMRT Pipe tools
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• SMRT Portal freezes
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• Smrt portal gmap "no such file or directory" error
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• SMRT Portal has dificulty connecting to the smrtportal mysql database
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• Smrt portal job status does not update
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• SMRT Portal jobs are being submitted as root
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• SMRT Portal Lost administrator password
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• SMRT Portal protocols
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• SMRT View does not launch
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• SMRT View does not show reads in the details panel
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• SMRT View is downloaded from the server every time you access it
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• SMRT View is slow
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• Smrtpipe.log error: java.lang.outofmemoryerror: java heap space
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• SMRT® Analysis Installation
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• SMRT® Portal job fails
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• SMRT® View does not launch
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• Specifying SMRT Pipe inputs
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• Specifying SMRT Pipe parameters
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• Step 3: Extract the Tarball
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• Step 5, Option 2: Run the Upgrade Script
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• Step 5: Run the Installation Script
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• Step 6: Set up Distributed Computing
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• Step 7: (New Installations Only) Set Up User Data Folders
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• Step 8: (New Installations Only) Set Up SMRT® Portal
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• Step 9: Start the SMRT Portal and Automatic Secondary Analysis Services
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• Stopping Celera Assembler jobs
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• The configure smrtanalysis.sh script fails
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• The head node is very slow when more than 20 jobs are running
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• The job is very slow
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• The Reference Repository
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• Timing problem with jobs
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• Troubleshooting configure_smrtanalysis.sh Script Fails
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• Troubleshooting the SMRT Analysis Suite
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• Troubleshooting_everything
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• User does not have the correct permissions to upgrade
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• Using the command line
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• Verify the installation
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• When using the sync option in SGE, you may see errors
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• You can start SMRT Portal, but cannot log in
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