Hi Ludo,
You should remove the column with rlnParticleName from the combined star
file (this is a quirk in relion-1.3, which will be fixed in relion-1.4).
Also, did you change all _rlnNrOfFrames entries to 6?
HTH,
S
On 11/24/2014 01:13 PM, Ludovic Renault wrote:
> Hi Sjors,
> I have performed movie processing in relion 1.3 on 2 different dataset of
> the same sample. Both have been collected under the same conditions.
> Now I have two subsets I wanted to merge.
> I just edited 1 star file so that the column assignment matches the othe
> star and then started a 3d ref on my merged star file (after copying movie
> particles into Particle folder).
> I get an error but am not sure if it's relion error or cluster error:
>
> [node104:28564] *** Process received signal ***
> [node104:28564] Signal: Segmentation fault (11)
> [node104:28564] Signal code: Address not mapped (1)
> [node104:28564] Failing at address: 0x1ecbd0c570
> [node80:15460] *** Process received signal ***
> [node80:15460] Signal: Segmentation fault (11)
> [node80:15460] Signal code: Address not mapped (1)
> [node80:15460] Failing at address: 0x161a536570
> [node107:25554] *** Process received signal ***
> [node107:25554] Signal: Segmentation fault (11)
> [node107:25554] Signal code: Address not mapped (1)
> [node107:25554] Failing at address: 0x17eeccb290
> [node107:25554] [ 0] /lib64/libpthread.so.0() [0x353120f500]
> [node107:25554] [ 1] /Software/linux/64bit/relion/relion-1.3-beta-3/
> lib/librelion-1.3.so.1(_ZN11MlOptimiser50doThreadPrecalculateShiftedImagesCtfsAndInvSigma2sEi+0xc0
> a) [0x7f0672f6588a]
> [node107:25554] [ 2] /Software/linux/64bit/relion/relion-1.3-beta-3/
> lib/librelion-1.3.so.1(_Z11_threadMainPv+0x1d) [0x7f0672f8c3cd]
> [node107:25554] [ 3] /lib64/libpthread.so.0() [0x3531207851]
> [node107:25554] [ 4] /lib64/libc.so.6(clone+0x6d) [0x3530ae811d]
> [node107:25554] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 6 with PID 25554 on node node107 exited on
> signal 11 (Segmentation fault).
> --------------------------------------------------------------------------
>
> The movies are 7 frames in one case and 6 in the other but both star files
> have been generated using 6 frames during movie processing.
> Could that be where the problem is?
> Thanks,
> Ludo
>
--
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
|