Troubleshooting Runtime Issues

This document lists some commonly faced issues related to GenPipes deployment and usage. These could be related to GenPipes deployment, software dependencies, environment setup or usage options.

The objective here is to list some commonly encountered issues and their fixes so that new users can benefit and focus more on using GenPipes. These are mostly run-time issues that a new user may face. If you are looking at troubleshooting GenPipes as part of feature development or contributing to GenPipes code, please refer to the Developer Guide and Troubleshooting Guide.

Contents

• Fatal Limit Error: Star RNA Sequencing
• Error: qsub command not found
• Runtime Failure: Job fails on worker nodes
• Error: RAP_ID not set
• Error: Missing Genomes and Annotations
• Error: While using STAR option in RNA Sequencing Pipeline
• Error: Newbie issue - the pipeline does not execute at all!
• Error: RNA Sequencing Star alignment - Out of Memory