Dear All,

I got errors during execution of  sidesplitter_wrapper.sh in RELION-3.1.1.
I paste the error messages at the end of this e-mail..

How should I do?

Best,
Hiroko Takazaki

＝　run.err　＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝
mv: `tmp3.dat' を stat できません: 
そのようなファイルやディレクトリはありません
mv: `tmp3.dat' を stat できません: 
そのようなファイルやディレクトリはありません
mv: `tmp3.dat' を stat できません: 
そのようなファイルやディレクトリはありません
mv: `tmp3.dat' を stat できません: 
そのようなファイルやディレクトリはありません
mv: `tmp3.dat' から `tmp1.dat' へ移動できません: 
そのようなファイルやディレクトリはありません
mv: `tmp3.dat' を stat できません: 
そのようなファイルやディレクトリはありません
/usr/local/relion-3.1/bin/relion_star_printtable: 行 14: tmp1.dat: 
そのようなファイルやディレクトリはありません
mv: `tmp3.dat' を stat できません: 
そのようなファイルやディレクトリはありません
mv: `tmp3.dat' を stat できません: 
そのようなファイルやディレクトリはありません
mv: `tmp3.dat' を stat できません: 
そのようなファイルやディレクトリはありません
join: tmp1.dat: そのようなファイルやディレクトリはありません

＝　run.out　＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝
  Auto-refine: Iteration= 3
  Auto-refine: Resolution= 7.40323 (no gain for 0 iter)
  Auto-refine: Changes in angles= 3.5251 degrees; and in offsets= 
1.10264 Angstroms (no gain for 0 iter)
  Estimating accuracies in the orientational assignment ...
    2/   2 sec 
............................................................~~(,_,">
  Auto-refine: Estimated accuracy angles= 9.85 degrees; offsets= 3.49313 
Angstroms
  Auto-refine: Angular step= 3.75 degrees; local searches= true
  Auto-refine: Offset search range= 3.375 Angstroms; offset step= 0.675 
Angstroms
  CurrentResolution= 7.40323 Angstroms, which requires 
orientationSampling of at least 4.23529 degrees for a particle of 
diameter 200 Angstroms
  Oversampling= 0 NrHiddenVariableSamplingPoints= 3045
  OrientationalSampling= 7.5 NrOrientations= 145
  TranslationalSampling= 1.35 NrTranslations= 21
=============================
  Oversampling= 1 NrHiddenVariableSamplingPoints= 97440
  OrientationalSampling= 3.75 NrOrientations= 1160
  TranslationalSampling= 0.675 NrTranslations= 84
=============================
  Expectation iteration 3
16.53/16.53 min 
............................................................~~(,_,">
  Averaging half-reconstructions up to 40 Angstrom resolution to prevent 
diverging orientations ...
  Note that only for higher resolutions the FSC-values are according to 
the gold-standard!
  Calculating solvent-corrected gold-standard FSC ...
   + randomize phases beyond:       7.17188 Angstroms
  Maximization ...
000/??? sec ~~(,_,"> [oo]
  + Making system call for external reconstruction: 
/usr/local/bin/sidesplitter_wrapper.sh 
Refine3D/job253/run_it003_half1_class001_external_reconstruct.star
NTHREADS=10
BODY_ID=
MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
23797 Checking for existence of 
Refine3D/job253/run_it003_class001_sidesplitter_running ...
NTHREADS=10
BODY_ID=
MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
23796 Checking for existence of 
Refine3D/job253/run_it003_class001_sidesplitter_running ...
23796 Created Refine3D/job253/run_it003_class001_sidesplitter_running
23796 2020年 12月 15日 火曜日 11:39:16 JST Running 
relion_external_reconstruct 
"Refine3D/job253/run_it003_half1_class001_external_reconstruct.star" > 
"Refine3D/job253/run_it003_half1_class001_external_reconstruct.out" 2> 
"Refine3D/job253/run_it003_half1_class001_external_reconstruct.err"
23797 Refine3D/job253/run_it003_class001_sidesplitter_running already exists
23797 2020年 12月 15日 火曜日 11:39:16 JST Running 
relion_external_reconstruct 
"Refine3D/job253/run_it003_half2_class001_external_reconstruct.star" > 
"Refine3D/job253/run_it003_half2_class001_external_reconstruct.out" 2> 
"Refine3D/job253/run_it003_half2_class001_external_reconstruct.err"
23796 Moving output file 
Refine3D/job253/run_it003_half1_class001_external_reconstruct.mrc to 
Refine3D/job253/run_it003_half1_class001_external_reconstruct_orig.mrc
Writing adjusted FSC curve to 
Refine3D/job253/run_it003_half1_class001_external_reconstruct_out.star
23796 2020年 12月 15日 火曜日 11:39:41 JST First reconstruct job finished; 
waiting for Refine3D/job253/run_it003_class001_sidesplitter_running to 
disappear
23796 2020年 12月 15日 火曜日 11:39:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running still exists; 
waiting...
23797 Moving output file 
Refine3D/job253/run_it003_half2_class001_external_reconstruct.mrc to 
Refine3D/job253/run_it003_half2_class001_external_reconstruct_orig.mrc
Writing adjusted FSC curve to 
Refine3D/job253/run_it003_half2_class001_external_reconstruct_out.star
23797 2020年 12月 15日 火曜日 11:39:41 JST Second reconstruct job finished; 
removing Refine3D/job253/run_it003_class001_sidesplitter_running
23797 2020年 12月 15日 火曜日 11:39:41 JST Waiting for 
Refine3D/job253/run_it003_class001_sidesplitter_running to reappear
23797 2020年 12月 15日 火曜日 11:39:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23796 2020年 12月 15日 火曜日 11:39:46 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running has disappeared. 
Moving on to SIDESPLITTER step.
23796 2020年 12月 15日 火曜日 11:39:46 JST Running OMP_NUM_THREADS=10 
/usr/local/bin/sidesplitter --v1 
"Refine3D/job253/run_it003_half1_class001_external_reconstruct_orig.mrc" 
--v2 
"Refine3D/job253/run_it003_half2_class001_external_reconstruct_orig.mrc" 
--rotfl --mask "MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc" > 
"Refine3D/job253/run_it003_class001_sidesplitter.out"
23797 2020年 12月 15日 火曜日 11:40:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23797 2020年 12月 15日 火曜日 11:41:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23797 2020年 12月 15日 火曜日 11:42:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23797 2020年 12月 15日 火曜日 11:43:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23797 2020年 12月 15日 火曜日 11:44:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23797 2020年 12月 15日 火曜日 11:45:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23797 2020年 12月 15日 火曜日 11:46:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23797 2020年 12月 15日 火曜日 11:47:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23797 2020年 12月 15日 火曜日 11:48:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running does not exist; 
waiting...
23796 Moving sidesplitter output 
Refine3D/job253/run_it003_half1_class001_external_reconstruct_orig_sidesplitter.mrc 
to Refine3D/job253/run_it003_half1_class001_external_reconstruct.mrc
23796 Moving sidesplitter output 
Refine3D/job253/run_it003_half2_class001_external_reconstruct_orig_sidesplitter.mrc 
to Refine3D/job253/run_it003_half2_class001_external_reconstruct.mrc
23796 2020年 12月 15日 火曜日 11:48:47 JST Finished sidesplitter. Recreating 
Refine3D/job253/run_it003_class001_sidesplitter_running to indicate job 
finished.
  + External reconstruction finished successfully, reading result back 
in ...
  + External reconstruction successfully updated external tau2 array ...
23797 2020年 12月 15日 火曜日 11:49:41 JST 
Refine3D/job253/run_it003_class001_sidesplitter_running has reappeared. 
Removing it and exiting
10.50/10.50 min 
............................................................~~(,_,">
・
・
・
  Auto-refine: Iteration= 9
  Auto-refine: Resolution= 4.33019 (no gain for 0 iter)
  Auto-refine: Changes in angles= 2.32281 degrees; and in offsets= 
0.676868 Angstroms (no gain for 2 iter)
  Estimating accuracies in the orientational assignment ...
    3/   3 sec 
............................................................~~(,_,">
  Auto-refine: Estimated accuracy angles= 5.175 degrees; offsets= 
1.97775 Angstroms
  Auto-refine: Angular step= 3.75 degrees; local searches= true
  Auto-refine: Offset search range= 3.375 Angstroms; offset step= 0.675 
Angstroms
  CurrentResolution= 4.33019 Angstroms, which requires 
orientationSampling of at least 2.46575 degrees for a particle of 
diameter 200 Angstroms
  Oversampling= 0 NrHiddenVariableSamplingPoints= 2940
  OrientationalSampling= 7.5 NrOrientations= 140
  TranslationalSampling= 1.35 NrTranslations= 21
=============================
  Oversampling= 1 NrHiddenVariableSamplingPoints= 94080
  OrientationalSampling= 3.75 NrOrientations= 1120
  TranslationalSampling= 0.675 NrTranslations= 84
=============================
  Expectation iteration 9
14.97/14.97 min 
............................................................~~(,_,">
  Averaging half-reconstructions up to 40 Angstrom resolution to prevent 
diverging orientations ...
  Note that only for higher resolutions the FSC-values are according to 
the gold-standard!
  Calculating solvent-corrected gold-standard FSC ...
   + randomize phases beyond:       7.40323 Angstroms
  Maximization ...
000/??? sec ~~(,_,"> [oo]
  + Making system call for external reconstruction: 
/usr/local/bin/sidesplitter_wrapper.sh 
Refine3D/job253/run_it009_half1_class001_external_reconstruct.star
NTHREADS=10
BODY_ID=
MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
22533 Checking for existence of 
Refine3D/job253/run_it009_class001_sidesplitter_running ...
NTHREADS=10
BODY_ID=
MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
22532 Checking for existence of 
Refine3D/job253/run_it009_class001_sidesplitter_running ...
22532 Created Refine3D/job253/run_it009_class001_sidesplitter_running
22532 2020年 12月 15日 火曜日 14:16:01 JST Running 
relion_external_reconstruct 
"Refine3D/job253/run_it009_half2_class001_external_reconstruct.star" > 
"Refine3D/job253/run_it009_half2_class001_external_reconstruct.out" 2> 
"Refine3D/job253/run_it009_half2_class001_external_reconstruct.err"
22533 Refine3D/job253/run_it009_class001_sidesplitter_running already exists
22533 2020年 12月 15日 火曜日 14:16:01 JST Running 
relion_external_reconstruct 
"Refine3D/job253/run_it009_half1_class001_external_reconstruct.star" > 
"Refine3D/job253/run_it009_half1_class001_external_reconstruct.out" 2> 
"Refine3D/job253/run_it009_half1_class001_external_reconstruct.err"
22533 Moving output file 
Refine3D/job253/run_it009_half1_class001_external_reconstruct.mrc to 
Refine3D/job253/run_it009_half1_class001_external_reconstruct_orig.mrc
Writing adjusted FSC curve to 
Refine3D/job253/run_it009_half1_class001_external_reconstruct_out.star
22532 Moving output file 
Refine3D/job253/run_it009_half2_class001_external_reconstruct.mrc to 
Refine3D/job253/run_it009_half2_class001_external_reconstruct_orig.mrc
Writing adjusted FSC curve to 
Refine3D/job253/run_it009_half2_class001_external_reconstruct_out.star
22532 2020年 12月 15日 火曜日 14:16:32 JST First reconstruct job finished; 
waiting for Refine3D/job253/run_it009_class001_sidesplitter_running to 
disappear
22532 2020年 12月 15日 火曜日 14:16:32 JST 
Refine3D/job253/run_it009_class001_sidesplitter_running still exists; 
waiting...
22533 2020年 12月 15日 火曜日 14:16:33 JST Second reconstruct job finished; 
removing Refine3D/job253/run_it009_class001_sidesplitter_running
22533 2020年 12月 15日 火曜日 14:16:33 JST Waiting for 
Refine3D/job253/run_it009_class001_sidesplitter_running to reappear
22533 2020年 12月 15日 火曜日 14:16:33 JST 
Refine3D/job253/run_it009_class001_sidesplitter_running does not exist; 
waiting...
22532 2020年 12月 15日 火曜日 14:16:37 JST 
Refine3D/job253/run_it009_class001_sidesplitter_running has disappeared. 
Moving on to SIDESPLITTER step.
22532 2020年 12月 15日 火曜日 14:16:37 JST Running OMP_NUM_THREADS=10 
/usr/local/bin/sidesplitter --v1 
"Refine3D/job253/run_it009_half1_class001_external_reconstruct_orig.mrc" 
--v2 
"Refine3D/job253/run_it009_half2_class001_external_reconstruct_orig.mrc" 
--rotfl --mask "MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc" > 
"Refine3D/job253/run_it009_class001_sidesplitter.out"
22533 2020年 12月 15日 火曜日 14:17:33 JST 
Refine3D/job253/run_it009_class001_sidesplitter_running does not exist; 
waiting...
22533 2020年 12月 15日 火曜日 14:18:33 JST 
Refine3D/job253/run_it009_class001_sidesplitter_running does not exist; 
waiting...
22533 2020年 12月 15日 火曜日 14:19:33 JST 
Refine3D/job253/run_it009_class001_sidesplitter_running does not exist; 
waiting...
22533 2020年 12月 15日 火曜日 14:20:33 JST 
Refine3D/job253/run_it009_class001_sidesplitter_running does not exist; 
waiting...
22533 2020年 12月 15日 火曜日 14:21:33 JST 
Refine3D/job253/run_it009_class001_sidesplitter_running does not exist; 
waiting...
22532 Moving sidesplitter output 
Refine3D/job253/run_it009_half1_class001_external_reconstruct_orig_sidesplitter.mrc 
to Refine3D/job253/run_it009_half1_class001_external_reconstruct.mrc
22532 Moving sidesplitter output 
Refine3D/job253/run_it009_half2_class001_external_reconstruct_orig_sidesplitter.mrc 
to Refine3D/job253/run_it009_half2_class001_external_reconstruct.mrc
22532 2020年 12月 15日 火曜日 14:22:30 JST Finished sidesplitter. Recreating 
Refine3D/job253/run_it009_class001_sidesplitter_running to indicate job 
finished.
22533 2020年 12月 15日 火曜日 14:22:33 JST 
Refine3D/job253/run_it009_class001_sidesplitter_running has reappeared. 
Removing it and exiting
  + External reconstruction finished successfully, reading result back 
in ...
  + External reconstruction successfully updated external tau2 array ...
6.63/6.63 min 
............................................................~~(,_,">
  Auto-refine: Iteration= 10
  Auto-refine: Resolution= 4.41346 (no gain for 1 iter)
  Auto-refine: Changes in angles= 2.31105 degrees; and in offsets= 
0.711281 Angstroms (no gain for 3 iter)
  Auto-refine: Refinement has converged, entering last iteration where 
two halves will be combined...
  Auto-refine: The last iteration will use data to Nyquist frequency, 
which may take more CPU and RAM.
  Estimating accuracies in the orientational assignment ...
   34/  34 sec 
............................................................~~(,_,">
  Auto-refine: Estimated accuracy angles= 4.965 degrees; offsets= 
1.96762 Angstroms
  Auto-refine: Angular step= 1.875 degrees; local searches= true
  Auto-refine: Offset search range= 3.375 Angstroms; offset step= 0.675 
Angstroms
  CurrentResolution= 4.41346 Angstroms, which requires 
orientationSampling of at least 2.51748 degrees for a particle of 
diameter 200 Angstroms
  Oversampling= 0 NrHiddenVariableSamplingPoints= 3150
  OrientationalSampling= 3.75 NrOrientations= 150
  TranslationalSampling= 1.35 NrTranslations= 21
=============================
  Oversampling= 1 NrHiddenVariableSamplingPoints= 100800
  OrientationalSampling= 1.875 NrOrientations= 1200
  TranslationalSampling= 0.675 NrTranslations= 84
=============================
  Expectation iteration 10
8.36/8.36 hrs 
............................................................~~(,_,">
  Averaging half-reconstructions up to 40 Angstrom resolution to prevent 
diverging orientations ...
  Note that only for higher resolutions the FSC-values are according to 
the gold-standard!
  Calculating solvent-corrected gold-standard FSC ...
   + randomize phases beyond:       6.75 Angstroms
  Maximization ...
000/??? sec ~~(,_,"> [oo]
  + Making system call for external reconstruction: 
/usr/local/bin/sidesplitter_wrapper.sh 
Refine3D/job253/run_it010_class001_external_reconstruct.star
NTHREADS=10
BODY_ID=
MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
28662 Checking for existence of 
Refine3D/job253/run_it010_class001_sidesplitter_running ...
28662 Created Refine3D/job253/run_it010_class001_sidesplitter_running
28662 2020年 12月 15日 火曜日 22:46:16 JST Running 
relion_external_reconstruct 
"Refine3D/job253/run_it010_class001_external_reconstruct.star" > 
"Refine3D/job253/run_it010_class001_external_reconstruct.out" 2> 
"Refine3D/job253/run_it010_class001_external_reconstruct.err"
28662 2020年 12月 15日 火曜日 22:57:19 JST Only a single reconstruction, 
removing Refine3D/job253/run_it010_class001_sidesplitter_running and 
exiting.
  + External reconstruction finished successfully, reading result back 
in ...
11.67/11.67 min 
............................................................~~(,_,">
  Auto-refine: Refinement has converged, stopping now...
  Auto-refine: + Final reconstruction from all particles is saved as: 
Refine3D/job253/run_class001.mrc
  Auto-refine: + Final model parameters are stored in: 
Refine3D/job253/run_model.star
  Auto-refine: + Final data parameters are stored in: 
Refine3D/job253/run_data.star
  Auto-refine: + Final resolution (already with masking) is: 4.02632

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