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Subject:

Re: sidesplitter error

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Thu, 24 Dec 2020 10:59:39 +0000

Content-Type:

text/plain

Parts/Attachments:
Parts/Attachments

text/plain (648 lines) 

Hi,

In the latest ver3.1 branch (not 3.1.1 in the master branch yet),
the race condition in relion_star_printtable has been fixed and
you shouldn't get this problem.

https://github.com/3dem/relion/commit/cfdec2616e40bdfad91e65efd856263d9537a15f

Does your problem persist in this branch?

Best regards,

Takanori Nakane

On 2020/12/24 9:33, Yongchan Lee wrote:
> Dear Takazaki-san,
> 
> I have seen this error before with SIDESPLITTER several times, but this error does not seem to cause any problem in the outcome. I am guessing this is 
> due to synchronization of two half sets - when refinement enters a SIDESPLITTER step, one of the two processes changes its behavior when the other is 
> processing the second half map. Probably the first iteration is so synchronized that the two processes start simultaneously, and either of them cannot 
> find a right file. This is just a wild guess, but reading the run.out, I gather the refinement finished successfully, did it?
> 
> I hope this helps.
> 
> Best wishes,
> Yongchan
> 
> On 2020/12/24 4:17, Hiroko Takazaki wrote:
>> Dear Nakane-san and All,
>>
>> Thank you for your reply.
>>
>> I re-ran the same job with setting of LC_ALL=C.
>> The error occurs during first iteration, and it seems to occur at random during subsequent iterations.
>> The error messages are pasted at the end of this e-mail.
>> Please check them.
>>
>> Sencerely yours,
>> Hiroko Takazaki
>>
>> ＝　run.err　＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝
>>  WARNING: FSC curve between unmasked maps never drops below 0.8. Using unmasked FSC as FSC_true...
>>  WARNING: This message should go away during the later stages of refinement!
>> mv: cannot stat 'tmp3.dat': No such file or directory    << @21:31 during it001
>> mv: cannot stat 'tmp3.dat': No such file or directory    << @21:31 during it001
>> mv: cannot stat 'tmp3.dat': No such file or directory    << @22:20 during it003
>> mv: cannot stat 'tmp3.dat': No such file or directory    << @22:20 during it003
>> mv: cannot stat 'tmp3.dat': No such file or directory    << @23:20 during it005
>> join: tmp1.dat: No such file or directory << @23:20 during it005
>> mv: cannot stat 'tmp3.dat': No such file or directory    << @23:47 during it006
>> mv: cannot stat 'tmp3.dat': No such file or directory    << @01:25 during it009
>> mv: cannot stat 'tmp3.dat': No such file or directory    << I'm sleeping...zzz.
>> mv: cannot stat 'tmp3.dat': No such file or directory
>> /usr/local/relion-3.1/bin/relion_star_printtable: line 7: tmp.dat: No such file or directory
>> /usr/local/relion-3.1/bin/relion_star_printtable: line 10: tmp.dat: No such file or directory
>> join: tmp1.dat: No such file or directory
>> /usr/local/relion-3.1/bin/relion_star_printtable: line 10: tmp.dat: No such file or directory
>> join: tmp2.dat: No such file or directory
>> mv: cannot stat 'tmp3.dat': No such file or directory
>> mv: cannot stat 'tmp3.dat': No such file or directory <<@04:15 during it013
>> ＝　run.out　＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝
>>  Auto-refine: Iteration= 1
>>  Auto-refine: Resolution= 20.8636 (no gain for 0 iter)
>>  Auto-refine: Changes in angles= 999 degrees; and in offsets= 999 Angstroms (no gain for 0 iter)
>>  Estimating accuracies in the orientational assignment ...
>>    1/   1 sec ............................................................~~(,_,">
>>  Auto-refine: Estimated accuracy angles= 17.34 degrees; offsets= 5.4405 Angstroms
>>  Auto-refine: WARNING: The angular accuracy is worse than 10 degrees, so basically you cannot align your particles (yet)!
>>  Auto-refine: WARNING: You probably need not worry if the accuracy improves during the next few iterations.
>>  Auto-refine: WARNING: However, if the problem persists it may lead to spurious FSC curves, so be wary of inflated resolution estimates...
>>  Auto-refine: WARNING: Sometimes it is better to tune resolution yourself by adjusting T in a 3D-classification with a single class.
>>  CurrentResolution= 20.8636 Angstroms, which requires orientationSampling of at least 11.6129 degrees for a particle of diameter 200 Angstroms
>>  Oversampling= 0 NrHiddenVariableSamplingPoints= 3150
>>  OrientationalSampling= 7.5 NrOrientations= 150
>>  TranslationalSampling= 1.35 NrTranslations= 21
>> =============================
>>  Oversampling= 1 NrHiddenVariableSamplingPoints= 100800
>>  OrientationalSampling= 3.75 NrOrientations= 1200
>>  TranslationalSampling= 0.675 NrTranslations= 84
>> =============================
>>  Expectation iteration 1
>> 8.83/8.83 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 ...
>>  Maximization ...
>> 000/??? sec ~~(,_,"> [oo]
>>  + Making system call for external reconstruction: /usr/local/bin/sidesplitter_wrapper.sh 
>> Refine3D/job268/run_it001_half1_class001_external_reconstruct.star
>> NTHREADS=10
>> BODY_ID=
>> MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
>> 18312 Checking for existence of Refine3D/job268/run_it001_class001_sidesplitter_running ...
>> 18312 Created Refine3D/job268/run_it001_class001_sidesplitter_running
>> 18312 Wed Dec 23 21:31:03 JST 2020 Running relion_external_reconstruct "Refine3D/job268/run_it001_half1_class001_external_reconstruct.star" > 
>> "Refine3D/job268/run_it001_half1_class001_external_reconstruct.out" 2> "Refine3D/job268/run_it001_half1_class001_external_reconstruct.err"
>> NTHREADS=10
>> BODY_ID=
>> MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
>> 18322 Checking for existence of Refine3D/job268/run_it001_class001_sidesplitter_running ...
>> 18322 Refine3D/job268/run_it001_class001_sidesplitter_running already exists
>> 18322 Wed Dec 23 21:31:04 JST 2020 Running relion_external_reconstruct "Refine3D/job268/run_it001_half2_class001_external_reconstruct.star" > 
>> "Refine3D/job268/run_it001_half2_class001_external_reconstruct.out" 2> "Refine3D/job268/run_it001_half2_class001_external_reconstruct.err"
>> 18322 Moving output file Refine3D/job268/run_it001_half2_class001_external_reconstruct.mrc to 
>> Refine3D/job268/run_it001_half2_class001_external_reconstruct_orig.mrc
>> 18312 Moving output file Refine3D/job268/run_it001_half1_class001_external_reconstruct.mrc to 
>> Refine3D/job268/run_it001_half1_class001_external_reconstruct_orig.mrc
>> Writing adjusted FSC curve to Refine3D/job268/run_it001_half1_class001_external_reconstruct_out.star
>> Writing adjusted FSC curve to Refine3D/job268/run_it001_half2_class001_external_reconstruct_out.star
>> 18322 Wed Dec 23 21:31:21 JST 2020 Second reconstruct job finished; removing Refine3D/job268/run_it001_class001_sidesplitter_running
>> 18312 Wed Dec 23 21:31:21 JST 2020 First reconstruct job finished; waiting for Refine3D/job268/run_it001_class001_sidesplitter_running to disappear
>> 18312 Wed Dec 23 21:31:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running still exists; waiting...
>> 18322 Wed Dec 23 21:31:21 JST 2020 Waiting for Refine3D/job268/run_it001_class001_sidesplitter_running to reappear
>> 18322 Wed Dec 23 21:31:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running does not exist; waiting...
>> 18312 Wed Dec 23 21:31:26 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running has disappeared. Moving on to SIDESPLITTER step.
>> 18312 Wed Dec 23 21:31:26 JST 2020 Running OMP_NUM_THREADS=10 /usr/local/bin/sidesplitter --v1 
>> "Refine3D/job268/run_it001_half1_class001_external_reconstruct_orig.mrc" --v2 
>> "Refine3D/job268/run_it001_half2_class001_external_reconstruct_orig.mrc" --rotfl --mask "MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc" > 
>> "Refine3D/job268/run_it001_class001_sidesplitter.out"
>> 18322 Wed Dec 23 21:32:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running does not exist; waiting...
>> 18322 Wed Dec 23 21:33:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running does not exist; waiting...
>> 18322 Wed Dec 23 21:34:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running does not exist; waiting...
>> 18322 Wed Dec 23 21:35:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running does not exist; waiting...
>> 18322 Wed Dec 23 21:36:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running does not exist; waiting...
>> 18322 Wed Dec 23 21:37:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running does not exist; waiting...
>> 18322 Wed Dec 23 21:38:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running does not exist; waiting...
>> 18322 Wed Dec 23 21:39:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running does not exist; waiting...
>> 18312 Moving sidesplitter output Refine3D/job268/run_it001_half1_class001_external_reconstruct_orig_sidesplitter.mrc to 
>> Refine3D/job268/run_it001_half1_class001_external_reconstruct.mrc
>> 18312 Moving sidesplitter output Refine3D/job268/run_it001_half2_class001_external_reconstruct_orig_sidesplitter.mrc to 
>> Refine3D/job268/run_it001_half2_class001_external_reconstruct.mrc
>> 18312 Wed Dec 23 21:39:58 JST 2020 Finished sidesplitter. Recreating Refine3D/job268/run_it001_class001_sidesplitter_running to indicate job finished.
>>  + External reconstruction finished successfully, reading result back in ...
>>  + External reconstruction successfully updated external tau2 array ...
>> 18322 Wed Dec 23 21:40:21 JST 2020 Refine3D/job268/run_it001_class001_sidesplitter_running has reappeared. Removing it and exiting
>> 9.42/9.42 min ............................................................~~(,_,">
>>  Auto-refine: Iteration= 2
>>  Auto-refine: Resolution= 10.9286 (no gain for 0 iter)
>>  Auto-refine: Changes in angles= 5.04092 degrees; and in offsets= 1.25273 Angstroms (no gain for 0 iter)
>>  Estimating accuracies in the orientational assignment ...
>>    0/   0 sec ............................................................~~(,_,">
>>  Auto-refine: Estimated accuracy angles= 9.23 degrees; offsets= 3.04425 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= 10.9286 Angstroms, which requires orientationSampling of at least 6.2069 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 2
>> 12.15/12.15 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:       7.65 Angstroms
>>  Maximization ...
>> 000/??? sec ~~(,_,"> [oo]
>>  + Making system call for external reconstruction: /usr/local/bin/sidesplitter_wrapper.sh 
>> Refine3D/job268/run_it002_half1_class001_external_reconstruct.star
>> NTHREADS=10
>> BODY_ID=
>> MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
>> NTHREADS=10
>> BODY_ID=
>> MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
>> 11324 Checking for existence of Refine3D/job268/run_it002_class001_sidesplitter_running ...
>> 11325 Checking for existence of Refine3D/job268/run_it002_class001_sidesplitter_running ...
>> 11324 Created Refine3D/job268/run_it002_class001_sidesplitter_running
>> 11325 Refine3D/job268/run_it002_class001_sidesplitter_running already exists
>> 11325 Wed Dec 23 21:53:13 JST 2020 Running relion_external_reconstruct "Refine3D/job268/run_it002_half1_class001_external_reconstruct.star" > 
>> "Refine3D/job268/run_it002_half1_class001_external_reconstruct.out" 2> "Refine3D/job268/run_it002_half1_class001_external_reconstruct.err"
>> 11324 Wed Dec 23 21:53:13 JST 2020 Running relion_external_reconstruct "Refine3D/job268/run_it002_half2_class001_external_reconstruct.star" > 
>> "Refine3D/job268/run_it002_half2_class001_external_reconstruct.out" 2> "Refine3D/job268/run_it002_half2_class001_external_reconstruct.err"
>> 11324 Moving output file Refine3D/job268/run_it002_half2_class001_external_reconstruct.mrc to 
>> Refine3D/job268/run_it002_half2_class001_external_reconstruct_orig.mrc
>> Writing adjusted FSC curve to Refine3D/job268/run_it002_half2_class001_external_reconstruct_out.star
>> 11324 Wed Dec 23 21:53:32 JST 2020 First reconstruct job finished; waiting for Refine3D/job268/run_it002_class001_sidesplitter_running to disappear
>> 11324 Wed Dec 23 21:53:32 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running still exists; waiting...
>> 11325 Moving output file Refine3D/job268/run_it002_half1_class001_external_reconstruct.mrc to 
>> Refine3D/job268/run_it002_half1_class001_external_reconstruct_orig.mrc
>> Writing adjusted FSC curve to Refine3D/job268/run_it002_half1_class001_external_reconstruct_out.star
>> 11325 Wed Dec 23 21:53:33 JST 2020 Second reconstruct job finished; removing Refine3D/job268/run_it002_class001_sidesplitter_running
>> 11325 Wed Dec 23 21:53:33 JST 2020 Waiting for Refine3D/job268/run_it002_class001_sidesplitter_running to reappear
>> 11325 Wed Dec 23 21:53:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running does not exist; waiting...
>> 11324 Wed Dec 23 21:53:37 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running has disappeared. Moving on to SIDESPLITTER step.
>> 11324 Wed Dec 23 21:53:37 JST 2020 Running OMP_NUM_THREADS=10 /usr/local/bin/sidesplitter --v1 
>> "Refine3D/job268/run_it002_half1_class001_external_reconstruct_orig.mrc" --v2 
>> "Refine3D/job268/run_it002_half2_class001_external_reconstruct_orig.mrc" --rotfl --mask "MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc" > 
>> "Refine3D/job268/run_it002_class001_sidesplitter.out"
>> 11325 Wed Dec 23 21:54:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running does not exist; waiting...
>> 11325 Wed Dec 23 21:55:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running does not exist; waiting...
>> 11325 Wed Dec 23 21:56:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running does not exist; waiting...
>> 11325 Wed Dec 23 21:57:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running does not exist; waiting...
>> 11325 Wed Dec 23 21:58:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running does not exist; waiting...
>> 11325 Wed Dec 23 21:59:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running does not exist; waiting...
>> 11325 Wed Dec 23 22:00:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running does not exist; waiting...
>> 11325 Wed Dec 23 22:01:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running does not exist; waiting...
>> 11324 Moving sidesplitter output Refine3D/job268/run_it002_half1_class001_external_reconstruct_orig_sidesplitter.mrc to 
>> Refine3D/job268/run_it002_half1_class001_external_reconstruct.mrc
>> 11324 Moving sidesplitter output Refine3D/job268/run_it002_half2_class001_external_reconstruct_orig_sidesplitter.mrc to 
>> Refine3D/job268/run_it002_half2_class001_external_reconstruct.mrc
>> 11324 Wed Dec 23 22:02:22 JST 2020 Finished sidesplitter. Recreating Refine3D/job268/run_it002_class001_sidesplitter_running to indicate job finished.
>> 11325 Wed Dec 23 22:02:33 JST 2020 Refine3D/job268/run_it002_class001_sidesplitter_running has reappeared. Removing it and exiting
>>  + External reconstruction finished successfully, reading result back in ...
>>  + External reconstruction successfully updated external tau2 array ...
>> 9.45/9.45 min ............................................................~~(,_,">
>>  Auto-refine: Iteration= 3
>>  Auto-refine: Resolution= 7.40323 (no gain for 0 iter)
>>  Auto-refine: Changes in angles= 3.53627 degrees; and in offsets= 1.10235 Angstroms (no gain for 0 iter)
>>  Estimating accuracies in the orientational assignment ...
>>    2/   2 sec ............................................................~~(,_,">
>>  Auto-refine: Estimated accuracy angles= 10.495 degrees; offsets= 3.42562 Angstroms
>>  Auto-refine: WARNING: The angular accuracy is worse than 10 degrees, so basically you cannot align your particles (yet)!
>>  Auto-refine: WARNING: You probably need not worry if the accuracy improves during the next few iterations.
>>  Auto-refine: WARNING: However, if the problem persists it may lead to spurious FSC curves, so be wary of inflated resolution estimates...
>>  Auto-refine: WARNING: Sometimes it is better to tune resolution yourself by adjusting T in a 3D-classification with a single class.
>>  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
>> 16.90/16.90 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/job268/run_it003_half1_class001_external_reconstruct.star
>> NTHREADS=10
>> BODY_ID=
>> MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
>> 5040 Checking for existence of Refine3D/job268/run_it003_class001_sidesplitter_running ...
>> NTHREADS=10
>> BODY_ID=
>> MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
>> 5041 Checking for existence of Refine3D/job268/run_it003_class001_sidesplitter_running ...
>> 5040 Created Refine3D/job268/run_it003_class001_sidesplitter_running
>> 5041 Refine3D/job268/run_it003_class001_sidesplitter_running already exists
>> 5040 Wed Dec 23 22:20:11 JST 2020 Running relion_external_reconstruct "Refine3D/job268/run_it003_half1_class001_external_reconstruct.star" > 
>> "Refine3D/job268/run_it003_half1_class001_external_reconstruct.out" 2> "Refine3D/job268/run_it003_half1_class001_external_reconstruct.err"
>> 5041 Wed Dec 23 22:20:11 JST 2020 Running relion_external_reconstruct "Refine3D/job268/run_it003_half2_class001_external_reconstruct.star" > 
>> "Refine3D/job268/run_it003_half2_class001_external_reconstruct.out" 2> "Refine3D/job268/run_it003_half2_class001_external_reconstruct.err"
>> 5040 Moving output file Refine3D/job268/run_it003_half1_class001_external_reconstruct.mrc to 
>> Refine3D/job268/run_it003_half1_class001_external_reconstruct_orig.mrc
>> 5041 Moving output file Refine3D/job268/run_it003_half2_class001_external_reconstruct.mrc to 
>> Refine3D/job268/run_it003_half2_class001_external_reconstruct_orig.mrc
>> Writing adjusted FSC curve to Refine3D/job268/run_it003_half2_class001_external_reconstruct_out.star
>> Writing adjusted FSC curve to Refine3D/job268/run_it003_half1_class001_external_reconstruct_out.star
>> 5040 Wed Dec 23 22:20:36 JST 2020 First reconstruct job finished; waiting for Refine3D/job268/run_it003_class001_sidesplitter_running to disappear
>> 5041 Wed Dec 23 22:20:36 JST 2020 Second reconstruct job finished; removing Refine3D/job268/run_it003_class001_sidesplitter_running
>> 5040 Wed Dec 23 22:20:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running still exists; waiting...
>> 5041 Wed Dec 23 22:20:36 JST 2020 Waiting for Refine3D/job268/run_it003_class001_sidesplitter_running to reappear
>> 5041 Wed Dec 23 22:20:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5040 Wed Dec 23 22:20:41 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running has disappeared. Moving on to SIDESPLITTER step.
>> 5040 Wed Dec 23 22:20:41 JST 2020 Running OMP_NUM_THREADS=10 /usr/local/bin/sidesplitter --v1 
>> "Refine3D/job268/run_it003_half1_class001_external_reconstruct_orig.mrc" --v2 
>> "Refine3D/job268/run_it003_half2_class001_external_reconstruct_orig.mrc" --rotfl --mask "MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc" > 
>> "Refine3D/job268/run_it003_class001_sidesplitter.out"
>> 5041 Wed Dec 23 22:21:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5041 Wed Dec 23 22:22:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5041 Wed Dec 23 22:23:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5041 Wed Dec 23 22:24:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5041 Wed Dec 23 22:25:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5041 Wed Dec 23 22:26:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5041 Wed Dec 23 22:27:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5041 Wed Dec 23 22:28:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5041 Wed Dec 23 22:29:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running does not exist; waiting...
>> 5040 Moving sidesplitter output Refine3D/job268/run_it003_half1_class001_external_reconstruct_orig_sidesplitter.mrc to 
>> Refine3D/job268/run_it003_half1_class001_external_reconstruct.mrc
>> 5040 Moving sidesplitter output Refine3D/job268/run_it003_half2_class001_external_reconstruct_orig_sidesplitter.mrc to 
>> Refine3D/job268/run_it003_half2_class001_external_reconstruct.mrc
>> 5040 Wed Dec 23 22:29:45 JST 2020 Finished sidesplitter. Recreating Refine3D/job268/run_it003_class001_sidesplitter_running to indicate job finished.
>>  + External reconstruction finished successfully, reading result back in ...
>>  + External reconstruction successfully updated external tau2 array ...
>> 5041 Wed Dec 23 22:30:36 JST 2020 Refine3D/job268/run_it003_class001_sidesplitter_running has reappeared. Removing it and exiting
>> 10.53/10.53 min ............................................................~~(,_,">
>> ・
>> ・
>> ・
>>  Auto-refine: Iteration= 5
>>  Auto-refine: Resolution= 4.5 (no gain for 0 iter)
>>  Auto-refine: Changes in angles= 2.57626 degrees; and in offsets= 0.636876 Angstroms (no gain for 0 iter)
>>  Estimating accuracies in the orientational assignment ...
>>    3/   3 sec ............................................................~~(,_,">
>>  Auto-refine: Estimated accuracy angles= 6.93 degrees; offsets= 2.33213 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= 4.5 Angstroms, which requires orientationSampling of at least 2.57143 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 5
>> 19.33/19.33 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/job268/run_it005_half1_class001_external_reconstruct.star
>> NTHREADS=10
>> BODY_ID=
>> MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
>> 28745 Checking for existence of Refine3D/job268/run_it005_class001_sidesplitter_running ...
>> NTHREADS=10
>> BODY_ID=
>> MASK=MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc
>> 28744 Checking for existence of Refine3D/job268/run_it005_class001_sidesplitter_running ...
>> 28744 Created Refine3D/job268/run_it005_class001_sidesplitter_running
>> 28745 Refine3D/job268/run_it005_class001_sidesplitter_running already exists
>> 28744 Wed Dec 23 23:19:32 JST 2020 Running relion_external_reconstruct "Refine3D/job268/run_it005_half2_class001_external_reconstruct.star" > 
>> "Refine3D/job268/run_it005_half2_class001_external_reconstruct.out" 2> "Refine3D/job268/run_it005_half2_class001_external_reconstruct.err"
>> 28745 Wed Dec 23 23:19:32 JST 2020 Running relion_external_reconstruct "Refine3D/job268/run_it005_half1_class001_external_reconstruct.star" > 
>> "Refine3D/job268/run_it005_half1_class001_external_reconstruct.out" 2> "Refine3D/job268/run_it005_half1_class001_external_reconstruct.err"
>> 28744 Moving output file Refine3D/job268/run_it005_half2_class001_external_reconstruct.mrc to 
>> Refine3D/job268/run_it005_half2_class001_external_reconstruct_orig.mrc
>> Writing adjusted FSC curve to Refine3D/job268/run_it005_half2_class001_external_reconstruct_out.star
>> 28745 Moving output file Refine3D/job268/run_it005_half1_class001_external_reconstruct.mrc to 
>> Refine3D/job268/run_it005_half1_class001_external_reconstruct_orig.mrc
>> Writing adjusted FSC curve to Refine3D/job268/run_it005_half1_class001_external_reconstruct_out.star
>> 28744 Wed Dec 23 23:20:02 JST 2020 First reconstruct job finished; waiting for Refine3D/job268/run_it005_class001_sidesplitter_running to disappear
>> 28744 Wed Dec 23 23:20:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running still exists; waiting...
>> 28745 Wed Dec 23 23:20:02 JST 2020 Second reconstruct job finished; removing Refine3D/job268/run_it005_class001_sidesplitter_running
>> 28745 Wed Dec 23 23:20:02 JST 2020 Waiting for Refine3D/job268/run_it005_class001_sidesplitter_running to reappear
>> 28745 Wed Dec 23 23:20:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28744 Wed Dec 23 23:20:07 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running has disappeared. Moving on to SIDESPLITTER step.
>> 28744 Wed Dec 23 23:20:07 JST 2020 Running OMP_NUM_THREADS=10 /usr/local/bin/sidesplitter --v1 
>> "Refine3D/job268/run_it005_half1_class001_external_reconstruct_orig.mrc" --v2 
>> "Refine3D/job268/run_it005_half2_class001_external_reconstruct_orig.mrc" --rotfl --mask "MaskCreate/job244/mask_Low25_T0001_Ex5_Se30.mrc" > 
>> "Refine3D/job268/run_it005_class001_sidesplitter.out"
>> 28745 Wed Dec 23 23:21:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28745 Wed Dec 23 23:22:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28745 Wed Dec 23 23:23:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28745 Wed Dec 23 23:24:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28745 Wed Dec 23 23:25:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28745 Wed Dec 23 23:26:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28745 Wed Dec 23 23:27:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28745 Wed Dec 23 23:28:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28745 Wed Dec 23 23:29:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running does not exist; waiting...
>> 28744 Moving sidesplitter output Refine3D/job268/run_it005_half1_class001_external_reconstruct_orig_sidesplitter.mrc to 
>> Refine3D/job268/run_it005_half1_class001_external_reconstruct.mrc
>> 28744 Moving sidesplitter output Refine3D/job268/run_it005_half2_class001_external_reconstruct_orig_sidesplitter.mrc to 
>> Refine3D/job268/run_it005_half2_class001_external_reconstruct.mrc
>> 28744 Wed Dec 23 23:29:54 JST 2020 Finished sidesplitter. Recreating Refine3D/job268/run_it005_class001_sidesplitter_running to indicate job finished.
>> 28745 Wed Dec 23 23:30:02 JST 2020 Refine3D/job268/run_it005_class001_sidesplitter_running has reappeared. Removing it and exiting
>>  + External reconstruction finished successfully, reading result back in ...
>>  + External reconstruction successfully updated external tau2 array ...
>> 10.60/10.60 min ............................................................~~(,_,">
>>
>>
>>
>> On 2020/12/23 20:32, Takanori Nakane wrote:
>>> Hi,
>>>
>>> First, please set LC_ALL=C to make error messages English.
>>> This also affects some behaviors of awk, which is used within
>>> the script.
>>>
>>> Next, "tmp3.dat" is a temporary file name in relion_star_printtable.
>>> Find where the error came from. Is this happening from the first iteration,
>>> or only at or after a certain iteration?
>>>
>>> Enable debug mode in the side splitter wrapper and inspect sidesplitter log files carefully.
>>> https://github.com/StructuralBiology-ICLMedicine/SIDESPLITTER/blob/master/sidesplitter_wrapper.sh#L56
>>>
>>> Best regards,
>>>
>>> Takanori Nakane
>>>
>>> On 2020/12/23 11:03, Hiroko Takazaki wrote:
>>>> 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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