Yongchan-san, Nakane-san and All,
Thank you for your kindness.
Refine3D with sidesplitter could finish without any error.
Now, my RELION is 3.1.1-commit-fd1bb7.
Thank you very much.
Have a nice holidy!!
Best wish,
Hiroko Takazaki
On 2020/12/24 19:59, Takanori Nakane wrote:
> 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���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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