Some runs complete with no reported PanGenomePipeline errors, but fail full converstion to PanACEA

[dbayles]

I'm experiencing some PanGenomePipeline runs where the pipeline appears to complete normally. (I.e. no errors were reported.) These runs are not able to be fully converted into the PanACEA output. (There is partial output.) I've been digging into the underlying scripts, but haven't been successful in pinning down the source of exactly what the underlying cause might be. There are couple of things that might provide some clues. In problematic runs, the Core.att and Core.attfGI files contain multiple cores identified (I.e. the first field in either file). I can't recall seeing multiple cores being identified in any normally performing runs. In normal runs, I've only seen a single core identified. The partial PanACEA conversion I get from the problematic runs only convert the data corresponding to the first core identified in the Core.att file. Is it O.K. to have more than one core being output in the Core.att and Core.attfGI files? If not then what might be causing multiple cores to be identified and output? If it is O.K. to have more than one core output, then is the problem that PanACEA's script is not handling multiple cores correctly? Any assistance in tracking down the problem and getting things running normally would be greatly appreciated.