When I use the run directive in snakemake (using python code) it doesn't produce any kind of error message for troubleshooting. Is this desired behavior? Am I missing something?
Here a minimal example using snakemake 7.8.3 and python 3.9.13.
I invoked snakemake with the -p option which in shell directive outputs the exact code as passed to the shell (but doesn't do anything for run directive I guess).
Snakefile:
def useless_function():
return[thisVariableAlsoDoesntExist]
rule all:
input: "final.txt"
rule test:
output: "final.txt"
run:
print(thisVariableDoesNotExist)
useless_function()
Stdout:
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
----- ------- ------------- -------------
all 1 1 1
test 1 1 1
total 2 1 1
Select jobs to execute...
[Mon Jul 25 18:59:13 2022]
rule test:
output: final.txt
jobid: 1
reason: Missing output files: final.txt
resources: tmpdir=/tmp
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2022-07-25T185913.188760.snakemake.log
Expected error message (when function and print command are executed directly on python console):
>>> print(thisVariableDoesNotExist)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
NameError: name 'thisVariableDoesNotExist' is not defined
>>> useless_function()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<stdin>", line 2, in useless_function
NameError: name 'thisVariableAlsoDoesntExist' is not defined
I suspect you are hitting this recent bug https://github.com/snakemake/snakemake/issues/1698.
If that is the case, you can downgrade to v7.6.2 or work around it, i.e. bear with it or wrap the the code in run in a self-contained script that you execute via shell. This latter is not a bad solution anyway since it keeps the code nicely isolated.