fix(fixing of issue #573): #580
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In some cases, when running the 3 classify steps independently, a genome may be filtered out in the alignment step. However, it's still present in the ani screening from the classify step and can have a ANI > 95% ( this can happen with partial genomes, where AF can still be high) Tk would try to report it twice in the summary file and would return an error. Instead we report it as classified with ani, but with a warning from the alignment step ( MSA < 10%). skani should reduce the number of such cases as it keep AF low for partial genomes.
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In some cases, when running the 3 classify steps independently, a genome may be filtered out in the alignment step. However, it's still present in the ani screening from the classify step and can have a ANI > 95% ( this can happen with partial genomes, where AF can still be high) Tk would try to report it twice in the summary file and would return an error. Instead we report it as classified with ani,
but with a warning from the alignment step ( MSA < 10%).
skani should reduce the number of such cases as it keep AF low for partial genomes.