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
> > >
> > >
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