MissingOutputException

The job reported success but Snakemake could not see the files it promised

why

Two very different causes share this message. On a cluster or network filesystem it is usually latency — the file exists but is not visible yet when Snakemake checks. Otherwise the rule genuinely wrote something other than what its output: declares.

what to do

On a shared filesystem raise --latency-wait (60 is a normal value). Otherwise run that rule's command by hand and compare what appears against the output: block. Note that \"Removing output files of failed job\" is a consequence — the real error is above it in the log.

Snakemake documented behaviour
This is one entry from BioErrors, a catalogue of bioinformatics error messages that point at the wrong thing. Every entry was traced to its real cause before it was written down.
If your error is not in it, paste it there and it gets traced and added.