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]>
> Sent: Friday, September 28, 2018 3:14:59 PM
> To: Zhaoming Su; [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]> on behalf of Domen Kampjut <[log in to unmask]>
> > Sent: Friday, September 28, 2018 7:45:40 AM
> > To: [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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