Snakemake cannot find output file, gives MissingOutputException while latency-wait is seemingly ignored - snakemake

Question

I have a simple rule to generate a file in Snakemake. Running snakemake results in an immediate error that it cannot find the generated file, even when --latency-wait is specified as a command line option.
However, this does seem to be a latency-related issue, as this Snakefile runs without problems on a local machine. The output below is on a system that has known latency problems.
Contents of Snakefile:
rule generate_file:
output:
"dummy.txt"
shell:
"head --bytes 1024 < /dev/zero | base64 > '{output}'; ls"
Commands:
$ snakemake --version
5.2.0
$ snakemake -p --latency-wait 10
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 generate_file
1
rule generate_file:
output: dummy.txt
jobid: 0
head --bytes 1024 < /dev/zero | base64 > 'dummy.txt'; ls
dummy.txt Snakefile
MissingOutputException in line 1 of /home/user/project/Snakefile:
[Errno 2] No such file or directory: ''
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Removing output files of failed job generate_file since they might be corrupted:
dummy.txt
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/user/project/.snakemake/log/2018-08-08T101648.774072.snakemake.log
Interestingly, the ls command shows the file is created and visible.

Answer 1

Your rule creates output file dummy.txt when used with snakemake version 5.2.2 and linux, and snakemake ends successfully. Perhaps it is a bug in version 5.2.0? I don't see anything about it in change logs though.
On related note, use of head in shell command used to result in non-zero exit status error. Apparently recent version behaves differently in this respect.