> 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/basespace/releases/previous-releases/2025/7.39.0.md). # 7.39.0 - BaseSpace Downloader 3.0 #### October 21, 2025 #### Features * Updated the BaseSpace Downloader to version 3.0. For more details, see [What's New](/basespace/overview/whats-new.md). * Added the 'DRAGEN Server' analysis location in Run Planning. Use this option to export the sample sheet to analyze sequencing data on a standalone DRAGEN server. * Manual mode runs from NovaSeq X and MiSeq i100 instruments without a sample sheet will now transition to 'complete' following upload. Previously these runs were marked as 'needs attention'. * Improved performance when loading the Microarray Analysis Setup tool. #### Bugs Fixed * Fixed an issue that could cause a "Separator must begin with the + sign" error when uploading a FASTQ file. * Fixed an issue that could cause a run or project transfer to become stuck. * Fixed an issue with the Analysis file browser that could cause files to display under the incorrect folder. * Fixed an issue that could cause a run status to stay 'Pending Analysis' after analysis aborts. * Fixed an issue in Microarray Analysis Setup where file upload was silently failing. * Fixed an issue in the Analysis list page Application filter that showed duplicated application names. * Fixed the Application filter in the Analysis list page to include the ICA Workflow Session Tracking app. * Fixed an issue when launching an analysis from the CLI where the default analysis name is not generated correctly. #### Known Issues * The copy and merge features are currently unavailable for samples generated by BCL Convert. --- # 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/basespace/releases/previous-releases/2025/7.39.0.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.