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Пока я сделала совсем простую замену в report и detail. Я выписываю путь до папки с выходом antismash, номер контига и номер перестановки. Надо на самом деле смотреть как по факту запускают и как разумнее всего выводить результат, но это уже сильно лучше, чем было изначально.