Dear Takanori,
Tried the latest fix (877139d9dd)
Still get the error after frame 9, and this time b-factors for the first
9 frames seem to make less sense than before, so it got worse in a way.
What exactly is the problem here, can you describe it briefly, please?
Thanks for your efforts!
Here are new B-factors:
# RELION; version 3.0-beta-2
data_perframe_bfactors
loop_
_rlnMovieFrameNumber #1
_rlnBfactorUsedForSharpening #2
_rlnFittedInterceptGuinierPlot #3
0 -1.01236 0.003240
1 -11.50108 0.001786
2 -16.51618 -0.02748
3 -22.32118 -0.01753
4 -28.48895 -0.00305
5 -31.38510 -0.02080
6 -34.23007 -0.01237
7 -40.68527 0.020047
8 -45.91777 0.041472
9 -49.76217 0.125882
10 -8.80873e+10 -inf
11 -8.80873e+10 -inf
And here are previous on the same data:
# RELION; version 3.0-beta-2
data_perframe_bfactors
loop_
_rlnMovieFrameNumber #1
_rlnBfactorUsedForSharpening #2
_rlnFittedInterceptGuinierPlot #3
0 -11.23603 0.049748
1 -0.08144 -0.21510
2 -0.08144 -0.25988
3 -1.65827 -0.30094
4 -6.20297 -0.29457
5 -12.73199 -0.27411
6 -18.13065 -0.24068
7 -21.96097 -0.23674
8 -26.33093 -0.20546
9 -29.74517 -0.11742
10 -8.80873e+10 -inf
11 -8.80873e+10 -inf
Prof. Leonid Sazanov
IST Austria
Am Campus 1
A-3400 Klosterneuburg
Austria
Phone: +43 2243 9000 3026
E-mail: [log in to unmask]
On 19/10/18 20:15, Takanori Nakane wrote:
> Hi,
>
> Jasenko made two more commits (0ad988f, 294ce0d) after I posted
> here yesterday. Did you try that? If the problem persists,
> we need more time to investigate. This is not an easy bug to fix.
>
> Best regards,
>
> Takanori Nakane
>
> On 2018/10/19 17:37, Leonid Sazanov wrote:
>> Dear all,
>>
>> We tried this fix, but still get the same error at the same frame.
>> Please let us know what else can be tried.
>>
>> Many thanks,
>> Leonid
>>
>> Prof. Leonid Sazanov
>> IST Austria
>> Am Campus 1
>> A-3400 Klosterneuburg
>> Austria
>>
>> Phone: +43 2243 9000 3026
>> E-mail: [log in to unmask]
>> Web: https://ist.ac.at/research/life-sciences/sazanov-group/
>>
>> On 17/10/2018 18:55, Takanori Nakane wrote:
>>> Dear all,
>>>
>>> Jasenko made a workaround for this issue.
>>> This is the latest commit (d9686b9) on our public repository.
>>>
>>> Please re-compile the program and 'continue' the job.
>>> If the trajectories also contain NaNs, it might still produce
>>> broken particles. If you notice it (i.e. Refine3D crashing),
>>> please let us know.
>>>
>>> Best regards,
>>>
>>> Takanori Nakane
>>>
>>>> Dear Liz,
>>>>
>>>> No, we did not.
>>>> I really hope developers will answer something, since now there are at
>>>> least three groups experiencing this problem.
>>>> Best wishes,
>>>> Leonid
>>>>
>>>> Prof. Leonid Sazanov
>>>> IST Austria
>>>> Am Campus 1
>>>> A-3400 Klosterneuburg
>>>> Austria
>>>>
>>>> Phone: +43 2243 9000 3026
>>>> E-mail: [log in to unmask]
>>>> Web: https://ist.ac.at/research/life-sciences/sazanov-group/
>>>>
>>>> On 13/10/2018 22:42, Liz Kellogg wrote:
>>>>> Hi Leonid,
>>>>>
>>>>> I'm experiencing the same issues. Did you ever get the issue
>>>>> resolved?
>>>>> Thanks
>>>>>
>>>>> Liz
>>>>>
>>>>> On Sat, Oct 13, 2018 at 10:42 AM Leonid Sazanov <[log in to unmask]
>>>>> <mailto:[log in to unmask]>> wrote:
>>>>>
>>>>> Dear Takanori and Jasenko,
>>>>>
>>>>> We still have not resolved this problem (reported by Domen
>>>>> below),
>>>>> which seems to happen to others as well.
>>>>> Does polishing normally work for K2 superresolution images if
>>>>> they
>>>>> have binned 2X in motioncor2?
>>>>> It seems that if we increase memory available the errors
>>>>> change but
>>>>> in the end it is always segmentation fault, and always on
>>>>> frame 10.
>>>>> Now we used 250 GB memory and still have this error.
>>>>> Would be great to resolve it.
>>>>> Many thanks
>>>>> Best wishes,
>>>>> Leonid
>>>>>
>>>>>
>>>>> Hi,
>>>>>
>>>>>
>>>>> Thanks for your suggestion. I have checked the directories
>>>>> but my
>>>>> FCC files are all of the same size as well (29344 bytes).
>>>>>
>>>>>
>>>>> Best,
>>>>>
>>>>> Domen
>>>>>
>>>>> On 29-Sep-18 0:48, Zhaoming Su wrote:
>>>>> >
>>>>> > Hi Takanori and Jasenko,
>>>>> >
>>>>> >
>>>>> > My FCC files have the same size.
>>>>> >
>>>>> >
>>>>> >
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103863_Data_10103657_10103658_20180910_1942_FCC_w0.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103863_Data_10103657_10103658_20180910_1942_FCC_w1.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103863_Data_10103667_10103668_20180910_1938_FCC_cc.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103863_Data_10103667_10103668_20180910_1938_FCC_w0.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103863_Data_10103667_10103668_20180910_1938_FCC_w1.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103571_10103572_20180910_1945_FCC_cc.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103571_10103572_20180910_1945_FCC_w0.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103571_10103572_20180910_1945_FCC_w1.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103579_10103580_20180910_1946_FCC_cc.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103579_10103580_20180910_1946_FCC_w0.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103579_10103580_20180910_1946_FCC_w1.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103589_10103590_20180910_1946_FCC_cc.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103589_10103590_20180910_1946_FCC_w0.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103589_10103590_20180910_1946_FCC_w1.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103603_10103604_20180910_1943_FCC_cc.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103603_10103604_20180910_1943_FCC_w0.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103603_10103604_20180910_1943_FCC_w1.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103612_10103613_20180910_1943_FCC_cc.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103612_10103613_20180910_1943_FCC_w0.mrc
>>>>> > -rw-r--r-- 1 suzm bd 13924 Sep 27 17:58
>>>>> FoilHole_10103864_Data_10103612_10103613_20180910_1943_FCC_w1.mrc
>>>>> >
>>>>> >
>>>>> > Best,
>>>>> >
>>>>> >
>>>>> > Zhaoming Su, Ph.D.
>>>>> >
>>>>> > Research Scientist, Bioengineering
>>>>> >
>>>>> > Stanford University
>>>>> > From: Takanori Nakane <[log in to unmask]
>>>>> <mailto:[log in to unmask]>>
>>>>> > Sent: Friday, September 28, 2018 3:14:59 PM
>>>>> > To: Zhaoming Su; [log in to unmask]
>>>>> <mailto:[log in to unmask]>
>>>>> > Cc: Jasenko Zivanov
>>>>> > Subject: Re: [ccpem] Bayesian Polishing b-factor fitting
>>>>> error
>>>>> >
>>>>> > Hi Domen and Zhaoming,
>>>>> >
>>>>> > I forward comments from Jasenko Zivanov (CC-ed),
>>>>> > the developer of Bayesian Polishing.
>>>>> >
>>>>> > Please make sure all FCC files under the job directory
>>>>> > have the same size.
>>>>> >
>>>>> > > Could it be that some of the (thousands of) partial FCC
>>>>> files
>>>>> (*_FCC_cc.mrc, *_FCC_w0/1.mrc) are damaged?
>>>>> > >
>>>>> > > Sjors changed the mrc-reader afterwards, so that it would
>>>>> refuse to load a corrupted image.
>>>>> > > That problem should be gone in the current version.
>>>>> > >
>>>>> > > I had observed a corrupted partial FCC file once myself.
>>>>> > > This could definitely introduce NaNs into the FCC
>>>>> computation.
>>>>> > >
>>>>> > > The way to diagnose this would be to check if there are
>>>>> unusually small files in the output-directory.
>>>>> > > All of them should be the same size.
>>>>> >
>>>>> > Best regards,
>>>>> >
>>>>> > Takanori Nakane
>>>>> >
>>>>> > On 2018/09/28 17:34, Zhaoming Su wrote:
>>>>> > > Hi All,
>>>>> > >
>>>>> > > I have the exact problem on multiple data sets collected as
>>>>> packed mrc from EPU, except they all fail at the second frame...
>>>>> > >
>>>>> > > # RELION; version 3.0-beta-2
>>>>> > >
>>>>> > > data_perframe_bfactors
>>>>> > >
>>>>> > > loop_
>>>>> > > _rlnMovieFrameNumber #1
>>>>> > > _rlnBfactorUsedForSharpening #2
>>>>> > > _rlnFittedInterceptGuinierPlot #3
>>>>> > >? ? ? ? ? ? ?0? ? ?-0.04828 6.304424e-05
>>>>> > >? ? ? ? ? ? ?1 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?2 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?3 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?4 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?5 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?6 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?7 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?8 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?9 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 10 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 11 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 12 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 13 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 14 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 15 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 16 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 17 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 18 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 19 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 20 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 21 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 22 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 23 -5.15980e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? 24 -5.15980e+10? ? ? ? ?-inf
>>>>> > >
>>>>> > >
>>>>> > >
>>>>> > > Best,
>>>>> > >
>>>>> > >
>>>>> > > Zhaoming Su, Ph.D.
>>>>> > >
>>>>> > > Research Scientist, Bioengineering
>>>>> > >
>>>>> > > Stanford University
>>>>> > >
>>>>> > > ________________________________
>>>>> > > From: Collaborative Computational Project in Electron
>>>>> cryo-Microscopy <[log in to unmask]
>>>>> <mailto:[log in to unmask]>>
>>>>> on behalf of Domen Kampjut <[log in to unmask]
>>>>> <mailto:[log in to unmask]>>
>>>>> > > Sent: Friday, September 28, 2018 7:45:40 AM
>>>>> > > To: [log in to unmask] <mailto:[log in to unmask]>
>>>>> > > Subject: [ccpem] Bayesian Polishing b-factor fitting error
>>>>> > >
>>>>> > > Dear All,
>>>>> > >
>>>>> > > I keep running into an error when trying to polish
>>>>> particles in
>>>>> > > relion3.0. Polishing job starts normally and estimated
>>>>> per-particle
>>>>> > > motion for all micrographs look very reasonable judging
>>>>> from
>>>>> the .eps
>>>>> > > files in the Micrographs subfolder. Estimating B-factors
>>>>> fails
>>>>> after
>>>>> > > 10th frame though (see the bfactors.star output below)
>>>>> and the
>>>>> job
>>>>> > > terminates with segmantation fault. I only see this
>>>>> error in
>>>>> the dataset
>>>>> > > collected with a K2 camera as packed .mrc movies using EPU.
>>>>> Polishing of
>>>>> > > Falcon-III movies works fine. Also, if I limit the
>>>>> polishing
>>>>> job to the
>>>>> > > first 9 frames the job completes normally. Please let me
>>>>> know
>>>>> if anyone
>>>>> > > else observed the same error and what you would need to
>>>>> reproduce it.
>>>>> > >
>>>>> > > Many thanks and best wishes,
>>>>> > >
>>>>> > > Domen Kampjut
>>>>> > >
>>>>> > >
>>>>> > >
>>>>> > >
>>>>> --------------------------------------------------------------
>>>>> > >
>>>>> > > data_perframe_bfactors
>>>>> > >
>>>>> > > loop_
>>>>> > > _rlnMovieFrameNumber #1
>>>>> > > _rlnBfactorUsedForSharpening #2
>>>>> > > _rlnFittedInterceptGuinierPlot #3
>>>>> > >? ? ? ? ? ? ? 0? ? -10.90545? ? ?0.048441
>>>>> > >? ? ? ? ? ? ? 1? ? ?-0.08144? ? ?-0.21434
>>>>> > >? ? ? ? ? ? ? 2? ? ?-0.08144? ? ?-0.26051
>>>>> > >? ? ? ? ? ? ? 3? ? ?-3.19811? ? ?-0.29255
>>>>> > >? ? ? ? ? ? ? 4? ? ?-5.69430? ? ?-0.29903
>>>>> > >? ? ? ? ? ? ? 5? ? -12.85827? ? ?-0.27141
>>>>> > >? ? ? ? ? ? ? 6? ? -19.60021? ? ?-0.24128
>>>>> > >? ? ? ? ? ? ? 7? ? -22.26604? ? ?-0.23126
>>>>> > >? ? ? ? ? ? ? 8? ? -28.06880? ? ?-0.19417
>>>>> > >? ? ? ? ? ? ? 9? ? -30.55454? ? ?-0.11258
>>>>> > >? ? ? ? ? ? ?10 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?11 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?12 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?13 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?14 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?15 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?16 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?17 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?18 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?19 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?20 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?21 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?22 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?23 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?24 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?25 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?26 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?27 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?28 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?29 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?30 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?31 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?32 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?33 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?34 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?35 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?36 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?37 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?38 -8.80873e+10? ? ? ? ?-inf
>>>>> > >? ? ? ? ? ? ?39 -8.80873e+10? ? ? ? ?-inf
>>>>> > >
>>>>> > >
>>>>> ########################################################################
>>>>>
>>>>> > >
>>>>> > > To unsubscribe from the CCPEM list, click the following
>>>>> link:
>>>>> > >
>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>>>>> > >
>>>>> > >
>>>>> ########################################################################
>>>>>
>>>>> > >
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>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
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>>>>> > To unsubscribe from the CCPEM list, click the following link:
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>>>>> To unsubscribe from the CCPEM list, click the following link:
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>>>>> ########################################################################
>>>>>
>>>>>
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>>>>
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>>>
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