Let PPanGGOLIN keep running if partition step fails #270
Description
It would be great if PPanGGOLIN could continue running even when the partition step fails, as it can still deliver valuable data like core and soft genomes. Originally, this scenario was handled by assigning data to the "unknown" partition, but this functionality has since been removed.
Right now, PPanGGOLIN prints a log if partitioning fails (a warning log since PR #269). If partitions completely failed, the pipeline fails latter with error reported in issue #262.
Improving this so it can keep going without crashing would make it more robust and useful.