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Dear Takanori, Thanks for the tip, I will try to find the culprit. Perhaps it may be possible in future to modify code such that error message lists problematic file? Thanks, Leo Prof. Leonid Sazanov IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: [log in to unmask] On 09/01/19 13:43, Takanori Nakane wrote: > Hi, > > Probably one of your MRCS files is truncated; for example, > your STAR file points to the 200-th image in the stack, but the > MRCS file contains only 190. > > Best regards, > > Takanori Nakane > >> Dear Sjors, >> >> As I mentioned, error messages looked a bit different each time, so I >> did not post them initially. >> >> Now I noticed that all of them eventually trace back to the same line in >> code, related to MRC file read/write: >> >> in: /localhome/schloegl/src/relion-3.0-beta/src/rwMRC.h, line 191 >> terminate called after throwing an instance of 'RelionError' >> >> This is the example command: >> >> `which relion_ctf_refine` --i Refine3D/job184/run_data.star --f >> PostProcess/job196/postprocess.star --m1 >> Refine3D/job184/run_half1_class001_unfil.mrc --m2 >> Refine3D/job184/run_half2_class001_unfil.mrc --mask >> MaskCreate/job156/mask_156.mrc --o CtfRefine/job226/ --kmin_defocus 30 >> --fit_defocus --range 2000 --fit_beamtilt --kmin_tilt 30 >> --only_do_unfinished? --j 8 >> >> With this set of particles (~30K, ~3.8 A resolution) CtfRefine always >> fails, but with another set from the same micrographs (170K, 3.9 A >> resolution) the same type of command works. >> >> I double checked that all files are in place and there are no issues >> with permissions, so I am not sure why MRC file read/writing fails. >> >> Thanks, >> >> Leo >> >> Prof. Leonid Sazanov >> IST Austria >> Am Campus 1 >> A-3400 Klosterneuburg >> Austria >> >> Phone: +43 2243 9000 3026 >> E-mail: [log in to unmask] >> >> On 07/01/19 09:04, Sjors Scheres wrote: >>> Dear Leo, >>> >>> I'm afraid this message does not provide a good starting point for a >>> follow-up investigation on our side. The below is not only for you, but >>> also for the community. >>> >>> When reporting errors, it is very useful for us to: >>> 1) know the exact command line arguments >>> 2) know the exact error >>> 3) know when that error occurs and when not >>> 4) (most useful) have a small test case you could share with us that >>> quickly and reproducibly leads to the error. >>> >>> In such cases we can relatively quickly find the error. Otherwise, it >>> may >>> take a long time... >>> >>> HTH, >>> Sjors >>> >>> >>>> Hi, recently using Relion3 build from 04 Dec with CtfRefine I >>>> constantly >>>> get cryptic errors which are different depending on whether I use >>>> several >>>> mpi and several threads or one mpi and several threads or even if just >>>> 1 >>>> mpi and 1 thread. Larger set of particles from the same set of images >>>> works fine, so that is really puzzling. >>>> Any info on what may help highly appreciated. >>>> Thanks! >>>> >>>> ######################################################################## >>>> >>>> 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