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giesselmann / STRique

Nanopore raw signal repeat detection pipeline
MIT License
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Test after installation failed #27

Closed rckeerthivasan closed 3 years ago

rckeerthivasan commented 3 years ago

Hi, I just installed the tool STRique and I ran the test command using 'python3 scripts/STRique_test.py' and I received the following errors. Thank you.

`EEEE

ERROR: test_Detection (main.DetectionTest)

Traceback (most recent call last): File "scripts/STRique_test.py", line 55, in test_Detection dt.add_target('c9orf72', repeat, prefix, suffix) File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 566, in add_target flankedRepeatHMM(repeat, prefix, suffix, self.pm, self.HMM_config), File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 402, in init self.build_model() File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 431, in build_model self.bake(merge='All') File "pomegranate/hmm.pyx", line 795, in pomegranate.hmm.HiddenMarkovModel.bake File "/home/ken/Kens/softwares.3/STRique/v1/lib64/python3.8/site-packages/networkx/classes/reportviews.py", line 718, in for nbr, dd in nbrs.items() RuntimeError: dictionary keys changed during iteration

====================================================================== ERROR: test_Interpolation (main.DetectionTest)

Traceback (most recent call last): File "scripts/STRique_test.py", line 75, in test_Interpolation dt.add_target('fmr1', repeat, prefix, suffix) File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 566, in add_target flankedRepeatHMM(repeat, prefix, suffix, self.pm, self.HMM_config), File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 402, in init self.build_model() File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 431, in build_model self.bake(merge='All') File "pomegranate/hmm.pyx", line 795, in pomegranate.hmm.HiddenMarkovModel.bake File "/home/ken/Kens/softwares.3/STRique/v1/lib64/python3.8/site-packages/networkx/classes/reportviews.py", line 718, in for nbr, dd in nbrs.items() RuntimeError: dictionary keys changed during iteration

====================================================================== ERROR: test_Modification (main.DetectionTest)

Traceback (most recent call last): File "scripts/STRique_test.py", line 114, in test_Modification dt.add_target('c9orf72', repeat, prefix, suffix) File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 566, in add_target flankedRepeatHMM(repeat, prefix, suffix, self.pm, self.HMM_config), File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 402, in init self.build_model() File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 431, in build_model self.bake(merge='All') File "pomegranate/hmm.pyx", line 795, in pomegranate.hmm.HiddenMarkovModel.bake File "/home/ken/Kens/softwares.3/STRique/v1/lib64/python3.8/site-packages/networkx/classes/reportviews.py", line 718, in for nbr, dd in nbrs.items() RuntimeError: dictionary keys changed during iteration

====================================================================== ERROR: test_Normalization (main.DetectionTest)

Traceback (most recent call last): File "scripts/STRique_test.py", line 93, in test_Normalization dt.add_target('c9orf72', repeat, prefix, suffix) File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 566, in add_target flankedRepeatHMM(repeat, prefix, suffix, self.pm, self.HMM_config), File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 402, in init self.build_model() File "/home/ken/Kens/softwares.3/STRique/STRique/scripts/STRique.py", line 431, in build_model self.bake(merge='All') File "pomegranate/hmm.pyx", line 795, in pomegranate.hmm.HiddenMarkovModel.bake File "/home/ken/Kens/softwares.3/STRique/v1/lib64/python3.8/site-packages/networkx/classes/reportviews.py", line 718, in for nbr, dd in nbrs.items() RuntimeError: dictionary keys changed during iteration

Ran 4 tests in 0.239s

FAILED (errors=4) `

giesselmann commented 3 years ago

Hi, looks like some version mismatch for me. Unfortunately are the versions of pomegranate and networkx crucial. Can you check that they meet the ones stated in requirements.txt or post the output of pip freeze here? I haven't tested STRique in py3.8 so far. Pay

rckeerthivasan commented 3 years ago

Hi,

Thank you for pointing it out. I reorganized the versions installed and it worked.

Ken.

Test GGCCCC repeat Test repeat length: 100 Test repeat length: 200 Test repeat length: 300 .Test GCG repeat Test repeat length: 100 Test repeat length: 200 Test repeat length: 300 .Test GGCCCC repeat Test repeat length: 100 Test repeat length: 200 Test repeat length: 300 .Test normalization on short prefix/suffix sequences Test repeat length: 10 Test repeat length: 20 Test repeat length: 30 Test repeat length: 40 Test repeat length: 50 Test repeat length: 60 Test repeat length: 70 Test repeat length: 80 Test repeat length: 90 .

Ran 4 tests in 22.581s

OK