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  Hi, I am running ScanNeo2 on Ubuntu (VirtualBox). I am using a MAF file as input, and my config.yaml is: [PASTE YOUR CONFIG HERE] When I run: snakemake --cores 4 --configfile config.yaml I get the following errors: 1. config file is not valid JSON or YAML 2. TypeError: string indices must be integers, not 'str' The MAF file exists and is valid (~14GB). Could you please help clarify the correct config format for using a MAF file as input? Thank you.

  fridahnyirenda4-star asked Apr 8, 2026 in Q&A · Closed · Unanswered

  

  

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