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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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