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 )