ProtectedOutputException is thrown for unprotected file #10
Description
Snakemake version
5.7.0
Describe the bug
When trying to re-execute a rule using snakemake -R <rulename>, snakemake throws an ProtectedOutputException even though the output file is not protected.
Downgrading to snakemake 5.6.0 solves the problem.
Minimal example
Consider the following Snakefile:
rule all:
input:
'out.txt'
rule dummy:
output:
'out.txt'
shell:
"""
touch {output}
"""
Executing it for the first time works as expected:
$ snakemake
Building DAG of jobs...
Using shell: /usr/local/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
1 dummy
2
[Tue Oct 8 13:57:07 2019]
rule dummy:
output: out.txt
jobid: 1
[Tue Oct 8 13:57:07 2019]
Finished job 1.
1 of 2 steps (50%) done
[Tue Oct 8 13:57:07 2019]
localrule all:
input: out.txt
jobid: 0
[Tue Oct 8 13:57:07 2019]
Finished job 0.
2 of 2 steps (100%) doneRe-executing dummy then fails:
$ snakemake -R dummy
Building DAG of jobs...
Using shell: /usr/local/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
1 dummy
2
ProtectedOutputException in line 5 of /private/tmp/example/Snakefile:
Write-protected output files for rule dummy:
out.txt