Calculating Average Amino Acid Identity (AAI) using CompareM
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Entering edit mode
4.7 years ago

Hi all,

I'm trying to calculate Average Amino-acid Identity (AAI) between a set of ~15 genomes. A program called CompareM (https://github.com/dparks1134/CompareM from the same set of minds who created the increasingly popular CheckM suite) was created to do this, among other things. It's made to run in a Linux environment, but I run macOS 10.13.3. Installation of dependencies and CompareM went alright. Gene-calling using Prodigal and Similiarity-search using DIAMOND work fine, but the last portion of the pipeline (using aai_calculator.py) gives null values for #homologs and AAI between genomes, although no errors are written to the log file. This error has been noted by macOS and linux users alike, and it's been noted by the authors that the error may have something to do with the implementation of the 'sort' command between different Linux flavors/macOS (https://github.com/dparks1134/CompareM/issues/14 ). Another macOS user of CompareM wrote a QuickStart protocol, also noting that the 'sed' and 'sort' commands require alteration when used by macOS (https://github.com/dparks1134/CompareM/issues/16 ). I've implemented these changes in similiarity_search.py, but AAI output is still null values. Has anyone used CompareM on macOS? Do any Linux users have any advice on possible conflicts between the system-type python calls written for linux, but run on macOS? I've linked to the GitHub repository for access to source and python scripts. Any help would be appreciated!

AAI ANI CheckM CompareM sort • 5.1k views
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4.3 years ago

@the.good.doctor.is.in,

Thanks, but I cited that link in my initial question. The conversation you've found is my own, with the user that I cited. Problem has been resolved.

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