ziyili20
commented
2 years ago I have the same error. Really hope if someone and provide a suggestion.
Open geng-lee opened 3 years ago
ziyili20
commented
2 years ago I have the same error. Really hope if someone and provide a suggestion.
neurbio
commented
1 year ago Same error with the test. Any suggestion?
neurbio
commented
1 year ago Same error with the test. Any suggestion?
Seems problem with samtools. RAN cd /root/anaconda3/envs/clipper3/lib ln -s libcrypto.so.1.1 libcrypto.so.1.0.0
The error is gone. However, test run still shows fail. Any help?
Traceback (most recent call last): File "/clipper/clipper/test/test_call_peak.py", line 57, in test_get_FDR_cutoff_mean self.assertAlmostEqual(result, 11, 2) # sometimes output 1 AssertionError: 12 != 11 within 2 places (1 difference)
Ran 36 tests in 25.394s
FAILED (failures=1)
The following error is reported. Can the clipper still be used normally
python -m unittest discover
python -m unittest discover .F....ERROR:root:Poisson cutoff failled float() argument must be a string or a number, not 'NoneType' .WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:883: ResourceWarning: subprocess 15250 is still running ResourceWarning, source=self)
WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/site-packages/pybedtools/bedtool.py:401: ResourceWarning: unclosed file <_io.BufferedReader name=34> decode_output=decode_output,
WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/site-packages/pybedtools/bedtool.py:1416: ResourceWarning: unclosed file <_io.BufferedReader name=32> for i in iterable:
53 22 0 0 .WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:883: ResourceWarning: subprocess 15293 is still running ResourceWarning, source=self)
53 22 0 0 .WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:689: ResourceWarning: unclosed file <_io.BufferedReader name=32> _cleanup()
WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:689: ResourceWarning: unclosed file <_io.BufferedReader name=34> _cleanup()
WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:883: ResourceWarning: subprocess 15342 is still running ResourceWarning, source=self)
WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:689: ResourceWarning: unclosed file <_io.BufferedReader name=32> _cleanup()
WARNING:py.warnings:/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/subprocess.py:689: ResourceWarning: unclosed file <_io.BufferedReader name=34> _cleanup()
..testing find sectionds .[(0, 2), (31, 63)] ....[2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 11.0, 9.0, 9.0, 9.0, 9.0, 9.0, 9.0, 9.0, 9.0, 0, 0, 0] ..[0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.06060606060606061, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 0.33333333333333326, 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ERROR: test_check_for_index (test_utils.Test) Performs unit tests on check_for_index function
Traceback (most recent call last): File "/backup/home/changxing/personal/LG/software/clipper-2.0.1/clipper/test/test_utils.py", line 27, in test_check_for_index handle = clipper.test_file("test_peakfinder.py") File "/backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/site-packages/clipper/init.py", line 30, in test_file raise ValueError("%s does not exist" % (fn)) ValueError: /backup/home/changxing/anaconda3/envs/clipper3/lib/python3.7/site-packages/clipper/test/data/test_peakfinder.py does not exist
====================================================================== FAIL: test_get_FDR_cutoff_mean (test_call_peak.Test) Performs unit tests on get_FDR_cutoff_mean function
Traceback (most recent call last): File "/backup/home/changxing/personal/LG/software/clipper-2.0.1/clipper/test/test_call_peak.py", line 57, in test_get_FDR_cutoff_mean self.assertAlmostEqual(result, 11, 2) # sometimes output 1 AssertionError: 12 != 11 within 2 places (1 difference)
Ran 36 tests in 28.989s
FAILED (failures=1, errors=1)