Hi Ran and Qiang,
I recently used the python script on my workstation (ubuntu 18.04, relion2). I encountered the similar error, then I solved with changing the scirpt at line 370 when it call ctffind:
relion_ctffindline = 'relion_run_ctffind --i ' + ctffindstarname + ' --o ' + outputstarname + ' --CS ' + str(Cs) + ' --HT ' + str(Voltage) + ' --ctfWin -1 --AmpCnst ' + str(AmpContrast) + ' --DStep ' + str(DPixSize) + ' --XMAG ' + str(Magnification) + ' --Box ' + str(BoxSize) + ' --dFMin ' + str(LowDefocusLimit) + ' --dFMax ' + str(HighDefocusLimit) + ' --FStep ' + str(DefocusStep) + ' --dAst ' + str(Astigmatism) + ' --ResMin ' + str(LowResLimit) + ' --ResMax ' + str(HighResLimit) + ' --ctffind_exe \"' + PathToCtffind + ' --old-school-input\"'
And also I used python3 to call the script, I have to use subprocess instead of commands module.
Hope it helps...
Hong
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