Error Message
AssertionError: Superpose reported a low Quality value when comparing models. This indicates the model could be significantly different in the re-run. assert 0.85 < 0.7331 + where 0.85 = <testSuite.ConsisCheck object at 0x119103c10>.superpose_cut
Stacktrace
testProjectPath = '/Users/jenkins/workspace/CCP4/series-8.0-osx/devtools/test-install/test/test101/ProjectZips/alphafold_test_3.ccp4_project.zip'
def test_eval(testProjectPath):
# Creating the test object runs i2
i2test = TSuite(testProjectPath)
i2test.HasItRun()
> i2test.AreResultsComp()
test101/RunTests/testSuite.py:73:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
test101/RunTests/testSuite.py:190: in AreResultsComp
ccheck.checkpdbs(job[0])
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <testSuite.ConsisCheck object at 0x119103c10>, jobnum = '1'
def checkpdbs(self, jobnum=None):
"""Run superpose and then check if it passes quality cut"""
self.skipo = []
print ("---------------------------------")
print ("Running Superpose for model check (job", jobnum, ")")
# First need to locate the pdbs (get folders first).
pdbfileso, pdbfilesn = self.__getI2OutputFiles(jobnum, "*.pdb")
warnmessage = "Warning: Number of pdb files does not match (between original and new test run), check"
warnings.warn(warnmessage)
for pdbo, pdbn in zip(pdbfileso, pdbfilesn):
ofilen = os.path.split(pdbn)[1]+"_sup_job_"+jobnum+".out"
tmp_outf = open(os.path.join(self.basefolder, ofilen), "w")
subprocess.call([superpose, pdbo, pdbn], stdout=tmp_outf)
tmp_outf.close()
with open(os.path.join(self.basefolder, ofilen), "r") as offy:
suout = offy.read()
if (re.search(r'Superposition was not achieved', suout) is not None) :
print ("CCP4 Superpose failed to work on the file comparison for :",
os.path.split(pdbo)[1] )
print ("If this model file does not contain a protein this is expected.")
self.skipo.append(pdbo)
else:
seares = re.findall(r'quality Q:\\s*(\\d+\\.\\d+)', suout)
if (len(seares) == 1):
quality = float(seares[0])
> assert (self.superpose_cut < quality <= 1.0), "Superpose reported a low Quality " \\
"value when comparing models. This indicates " \\
"the model could be significantly different " \\
"in the re-run."
E AssertionError: Superpose reported a low Quality value when comparing models. This indicates the model could be significantly different in the re-run.
E assert 0.85 < 0.7331
E + where 0.85 = <testSuite.ConsisCheck object at 0x119103c10>.superpose_cut
test101/RunTests/testSuite.py:358: AssertionError
Standard Output
Errors Reported by main ccp4i2 code (shown for information purposes)
job_1 CPdbDataFile #x1B[32m315#x1B[0m OK XYZOUT: Both compared objects are null
job_1 CPdbDataFile #x1B[33m308#x1B[0m ERROR XYZFILES[0]: Files failed checksum comparison /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3/CCP4_JOBS/job_1/converted_model.pdb : /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3_rerun_23-07-09-00-08/CCP4_JOBS/job_1/converted_model.pdb
job_1 CPdbDataFile #x1B[33m308#x1B[0m ERROR XYZFILES[1]: Files failed checksum comparison /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3/CCP4_JOBS/job_1/converted_model_chainA1.pdb : /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3_rerun_23-07-09-00-08/CCP4_JOBS/job_1/converted_model_chainA1.pdb
job_1 CPdbDataFile #x1B[33m308#x1B[0m ERROR XYZFILES[2]: Files failed checksum comparison /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3/CCP4_JOBS/job_1/converted_model_chainA2.pdb : /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3_rerun_23-07-09-00-08/CCP4_JOBS/job_1/converted_model_chainA2.pdb
job_1 CPdbDataFile #x1B[33m308#x1B[0m ERROR XYZFILES[3]: Files failed checksum comparison /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3/CCP4_JOBS/job_1/converted_model_chainA3.pdb : /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3_rerun_23-07-09-00-08/CCP4_JOBS/job_1/converted_model_chainA3.pdb
job_2 CPdbDataFile #x1B[32m315#x1B[0m OK XYZOUT: Both compared objects are null
job_2 CPdbDataFile #x1B[32m300#x1B[0m OK XYZFILES[0]: Passed
job_3 CPdbDataFile #x1B[32m315#x1B[0m OK XYZOUT: Both compared objects are null
job_3 CPdbDataFile #x1B[32m300#x1B[0m OK XYZFILES[0]: Passed
job_4 CPdbDataFile #x1B[32m315#x1B[0m OK XYZOUT: Both compared objects are null
job_4 CPdbDataFile #x1B[32m300#x1B[0m OK XYZFILES[0]: Passed
job_5 CPdbDataFile #x1B[32m315#x1B[0m OK XYZOUT: Both compared objects are null
job_5 CPdbDataFile #x1B[33m308#x1B[0m ERROR XYZFILES[0]: Files failed checksum comparison /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3/CCP4_JOBS/job_5/converted_model.pdb : /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3_rerun_23-07-09-00-08/CCP4_JOBS/job_5/converted_model.pdb
job_5 CPdbDataFile #x1B[33m308#x1B[0m ERROR XYZFILES[1]: Files failed checksum comparison /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3/CCP4_JOBS/job_5/converted_model_chainA1.pdb : /tmp/tmp_nnfbun9ialphafold_test_3/alphafold_test_3_rerun_23-07-09-00-08/CCP4_JOBS/job_5/converted_model_chainA1.pdb
job_6 CPdbDataFile #x1B[32m315#x1B[0m OK XYZOUT: Both compared objects are null
job_6 CPdbDataFile #x1B[32m300#x1B[0m OK XYZFILES[0]: Passed
Initialising Consistency Checks
ccp4i2 test job ran in folder /tmp/tmp_nnfbun9ialphafold_test_3
Review Job : 1
---------------------------------
Running Superpose for model check (job 1 )