Troubleshooting

• Throubleshooting the installation
• Troubleshooting general problems
• Troubleshooting the BAM Pipeline
  • Troubleshooting BAM pipeline makefiles
  • Troubleshooting AdapterRemoval
  • Troubleshooting BWA
  • Troubleshooting validation of BAM files
• Troubleshooting the Phylogenetic Pipeline
• Troubleshooting the Zonkey Pipeline

For troubleshooting of individual pipelines, please see the BAM pipeline Troubleshooting the BAM Pipeline section, the Phylo pipeline Troubleshooting the Phylogenetic Pipeline section, and the Zonkey pipeline Troubleshooting the Zonkey Pipeline section.