Please report
If an input readslist file for the -pool option contains only single-end reads, stage 1 will still run to the end.
Technically, RNA-Bloom should exit with an error indicating "pooled assembly of single-end reads is not supported."
I can also emphasize this (and explain why) in the readme section for -pool option:
https://github.com/bcgsc/RNA-Bloom#file-format-for-the--pool-option