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Created July 8, 2022 14:43
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(test-snakemake-wrappers) ilya@f346m-7eff66 snakemake-wrappers % pytest test.py -v -k cooltools
======================================================================= test session starts ========================================================================
platform darwin -- Python 3.10.5, pytest-7.1.2, pluggy-1.0.0 -- /Users/ilya/opt/anaconda3/envs/test-snakemake-wrappers/bin/python
cachedir: .pytest_cache
rootdir: /Users/ilya/Projects/snakemake-wrappers
collected 380 items / 379 deselected / 1 selected
test.py::test_cooltools_insulation FAILED [100%]
============================================================================= FAILURES =============================================================================
____________________________________________________________________ test_cooltools_insulation _____________________________________________________________________
@skip_if_not_modified
def test_cooltools_insulation():
> run(
"bio/cooltools/insulation",
["snakemake", "--cores", "1", "CN_1000000.insulation.tsv", "--use-conda", "-F"],
)
test.py:1488:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
test.py:121: in run
raise e
test.py:102: in run
subprocess.check_call(cmd)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['snakemake', '--cores', '1', 'CN_1000000.insulation.tsv', '--use-conda', '-F', ...],), kwargs = {}, retcode = 1
cmd = ['snakemake', '--cores', '1', 'CN_1000000.insulation.tsv', '--use-conda', '-F', ...]
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['snakemake', '--cores', '1', 'CN_1000000.insulation.tsv', '--use-conda', '-F', '--wrapper-prefix', 'file:///var/folders/rw/zbvfx5yd0f59ymh9tnpvkpsw0000gr/T/tmp53ni5m21/', '--conda-cleanup-pkgs', '--printshellcmds']' returned non-zero exit status 1.
../../opt/anaconda3/envs/test-snakemake-wrappers/lib/python3.10/subprocess.py:369: CalledProcessError
----------------------------------------------------------------------- Captured stderr call -----------------------------------------------------------------------
Building DAG of jobs...
WorkflowError:
Failed to open source file ../environment.yaml
FileNotFoundError: [Errno 2] No such file or directory: '../environment.yaml'
grep: invalid option -- P
usage: grep [-abcdDEFGHhIiJLlMmnOopqRSsUVvwXxZz] [-A num] [-B num] [-C[num]]
[-e pattern] [-f file] [--binary-files=value] [--color=when]
[--context[=num]] [--directories=action] [--label] [--line-buffered]
[--null] [pattern] [file ...]
Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
BrokenPipeError: [Errno 32] Broken pipe
===================================================================== short test summary info ======================================================================
FAILED test.py::test_cooltools_insulation - subprocess.CalledProcessError: Command '['snakemake', '--cores', '1', 'CN_1000000.insulation.tsv', '--use-conda', '-F...
================================================================ 1 failed, 379 deselected in 4.06s =================================================================
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