Hi Zhaoming Su,
One thing to try would be
relion_image_handler --stats --i
Movies/FoilHole_8023171_Data_8019792_8019793_20180908_1922.mrcs
and see if you get any NaNs or INFs there.
Also, you could just display the frames of those movies using
relion_display --i
Movies/FoilHole_8023171_Data_8019792_8019793_20180908_1922.mrcs and see
if something stands out.
If you do see something strange, please let us know. We might be
interested in having a look at such movies, as more people are reporting
similar problems.
HTH,
Sjors
On 10/22/2018 11:27 PM, Zhaoming Su wrote:
>
> Hi Jasenko and Takanori,
>
>
> Thanks so much for the commits, I am now able to have two of my
> datasets to finish polishing and output shiny.star files. In both
> cases I have a small portion (6 out of 5500 and 105 out of 7500
> movies) having the following message in the run.err file:
>
>
> NaNs detected in
> Polish/job033/Movies/FoilHole_8023171_Data_8019792_8019793_20180908_1922!
> Please inspect this movie.
>
>
> I wonder if this was the reason that I encountered the previous
> problem, and how should I inspect the movies? Sorry if similar
> questions have already been answered in previous topics. Thanks again
> for your help!
>
>
> 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 Takanori Nakane
> <[log in to unmask]>
> *Sent:* Friday, October 19, 2018 11:15:49 AM
> *To:* [log in to unmask]
> *Subject:* Re: [ccpem] Bayesian Polishing b-factor fitting error
>
> 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
> >>>> > >
> >>>> > >
> >>>>
> >>>>
> ########################################################################
> >>>>
> >>>> > >
> >>>> > > To unsubscribe from the CCPEM list, click the following
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> >>>
> >>>
> ########################################################################
> >>>
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> >>
> >>
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--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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