> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/troubleshooting.md). # Troubleshooting ## Help ### stopping analysis Pressing Ctrl+C during a DRAGEN step stops the currently running analysis and might cause an FPGA error. To recover from an FPGA error, shut down and restart the server. ### using a non-root user CAUTION: Do not run analyses as the root user as it can lead to permissions issues when managing data generated by the software. ### using ssh When running the analysis software using SSH, Illumina recommends using additional software to prevent unexpected termination of analysis. Illumina recommends `screen` and `tmux`. ### using DAM The pipeline depends on the DRAGEN Application Manager. For issues related to the DRAGEN Application Manager installation, refer to the DRAGEN Application Manager installation guide. * Ensure DRAGEN App Manager is running properly. ### using docker * Ensure Docker is running properly. For docker configuration help, please check the [DRAGEN Application Manager installation guide](https://help.dragen.illumina.com/reference/dragen-application-manager) and [docker.org documentation](https://docs.docker.com/reference/cli/dockerd). --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/dragen-clinical-research-apps/readme/dragen-solid-wgs-tn-pipeline/troubleshooting.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.