Scipion relion.tests.test_protocols_3d - TestRelionCalculateFSC.test_fsc_work_free failes with eman2 2.99.55

[wlugmayr]

==> Testing relion - calculate fsc:

*************** last 50 lines of STD ERR *********************

Traceback (most recent call last):
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/eman-2.99.55/bin/e2pdb2mrc.py", line 222, in main
y=float(line[38:46])
^^^^^^^^^^^^^^^^^^
ValueError: could not convert string to float: '6 55.727'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/eman-2.99.55/bin/e2pdb2mrc.py", line 476, in
main()
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/eman-2.99.55/bin/e2pdb2mrc.py", line 227, in main
print(a,aseq,resol,x,y,z)
^
UnboundLocalError: cannot access local variable 'y' where it is not associated with a value
Traceback (most recent call last):
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 211, in run
self._run()
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 261, in _run
resultFiles = self._runFunc()
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 257, in _runFunc
return self._func(*self._args)
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_calculate_fsc.py", line 139, in convertInputStep
self._model2Map(self.model_half1.get().getFileName(),
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/protocol_calculate_fsc.py", line 232, in _model2Map
runJob(self._log, eman2.Plugin.getProgram('e2pdb2mrc.py'), args,
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 57, in runJob
return runCommand(command, env=env, cwd=cwd, executable=executable)
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 72, in runCommand
check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' source /gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/etc/profile.d/conda.sh&& conda activate eman-2.99.55 && e2pdb2mrc.py Runs/000167_ProtImportPdb/extra/5ni1.cif Runs/000293_ProtRelionCalculateFSC/tmp/input_model_half1.mrc --box 100 --apix 1.050' returned non-zero exit status 1.
Protocol failed: Command ' source /gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/etc/profile.d/conda.sh&& conda activate eman-2.99.55 && e2pdb2mrc.py Runs/000167_ProtImportPdb/extra/5ni1.cif Runs/000293_ProtRelionCalculateFSC/tmp/input_model_half1.mrc --box 100 --apix 1.050' returned non-zero exit status 1.

*************** end of STD ERR *********************

[ FAILED ] TestRelionCalculateFSC.test_fsc_work_free

Traceback (most recent call last):
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
yield
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/unittest/case.py", line 676, in run
self._callTestMethod(testMethod)
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
method()
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/tests/test_protocols_3d.py", line 99, in test_fsc_work_free
self.launchProtocol(calcRun)
File "/gpfs/cssb/software/rhel9/x86_64/scipion/3.x/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/tests/tests.py", line 120, in launchProtocol
raise Exception("Protocol %s execution failed. See last log lines above for more details." % prot.getRunName())
Exception: Protocol relion - calculate fsc execution failed. See last log lines above for more details.