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I 've been using Snakemake with Tibanna for some time now without any problem. However, it seems that I cannot make Snakemake v7.0.0 or higher work with Tibanna (see traceback below). It works fine, though, with Snakemake v6.15.5. Any idea what's wrong? Maybe it has something to do with Snakemake v7.0.0 requiring at least Python v3.7?
Logs
Traceback (most recent call last):
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/utils.py", line 430, in format
return fmt.format(_pattern, *args, **variables)
File "/usr/lib/python3.9/string.py", line 161, in format
return self.vformat(format_string, args, kwargs)
File "/usr/lib/python3.9/string.py", line 165, in vformat
result, _ = self._vformat(format_string, args, kwargs, used_args, 2)
File "/usr/lib/python3.9/string.py", line 205, in _vformat
obj, arg_used = self.get_field(field_name, args, kwargs)
File "/usr/lib/python3.9/string.py", line 270, in get_field
obj = self.get_value(first, args, kwargs)
File "/usr/lib/python3.9/string.py", line 227, in get_value
return kwargs[key]
KeyError: 'job_specific_args'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/__init__.py", line 714, in snakemake
success = workflow.execute(
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/workflow.py", line 1097, in execute
success = self.scheduler.schedule()
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/scheduler.py", line 540, in schedule
self.run(runjobs)
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/scheduler.py", line 588, in run
executor.run_jobs(
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 153, in run_jobs
self.run(
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 2360, in run
tibanna_input = self.make_tibanna_input(job)
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 2344, in make_tibanna_input
self.add_command(job, tibanna_args, tibanna_config)
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 2221, in add_command
command = self.format_job_pattern(
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 375, in format_job_pattern
cmd = format(
File "/home/dimitris/Tmp/test_smk/venv/lib/python3.9/site-packages/snakemake/utils.py", line 432, in format
if str(ex).strip("'") in variables["wildcards"].keys():
KeyError: 'wildcards'
Minimal example
Snakefile (under workflow/):
ID = ['SAMPLE1', 'SAMPLE2']
rule all:
input:
tag = expand('results/TEST/{id}/{id}.txt', id = ID)
rule my_rule:
output:
tag = 'results/TEST/{id}/{id}.txt'
shell: "touch {output.tag}"
Snakemake version: 7.1.1
Describe the bug
I 've been using Snakemake with Tibanna for some time now without any problem. However, it seems that I cannot make Snakemake v7.0.0 or higher work with Tibanna (see traceback below). It works fine, though, with Snakemake v6.15.5. Any idea what's wrong? Maybe it has something to do with Snakemake v7.0.0 requiring at least Python v3.7?
Logs
Minimal example
Snakefile
(underworkflow/
):Profile
config.yaml
(underworkflow/config/aws/
):Run as:
snakemake --jobs 2 --profile wokflow/config/aws/ -n
(works fine)Run as:
snakemake --jobs 2 --profile wokflow/config/aws/
(see traceback above)Additional context None
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