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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 link: >> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 >> > > >> > >> > >> > 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 link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 >> >> ######################################################################## >> >> 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 link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 > ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1