> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.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 by asking a question. Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters: ``` GET https://help.bioinsight.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 what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case. 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.