Dear Sjors,
I am encountering an error when I try to launch autorefine "continue old
run" with movies. Actually the image number in the error reported below
change...
What would you suggest?
Another question: can the grouping procedure be coupled with the movie-
refinement?
Thank you so much,
Matteo
Expectation iteration 21
10.93/50.82 min ............~~(,_,">master encountered error: readMRC:
Image number 73 exceeds stack size 72
File: ./src/rwMRC.h line: 189
+++ RELION: command line arguments (with defaults for optional ones
between parantheses) +++
====== Continue options =====
--continue : _optimiser.star file of the
iteration after which to continue
====== General options =====
--o (OLD_ctX) : Output rootname
--iter (OLD) : Maximum number of iterations to perform
--tau2_fudge (OLD) : Regularisation parameter (values
higher than 1 give more weight to the data)
--flatten_solvent (OLD) : Switch on masking on the references?
--solvent_mask (OLD) : User-provided mask for the references
--solvent_mask2 (OLD) : User-provided secondary mask
--tau (OLD) : STAR file with input tau2-spectrum
(to be kept constant)
--particle_diameter (OLD) : Diameter of the circular mask that
will be applied to the experimental images (in Angstroms)
--join_random_halves (false) : Join previously split random halves
again (typically to perform a final reconstruction).
====== Re-align movie frames =====
--realign_movie_frames () : Input STAR file with the movie frames
--nr_frames_prior (5) : Number of movie frames to calculate
running-average priors
--movie_frames_running_avg (3) : Number of movie frames in each
running average
====== Orientations =====
--oversampling (OLD) : Adaptive oversampling order to
speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (OLD) : Healpix order for the angular
sampling rate on the sphere (before oversampling):
hp2=15deg, hp3=7.5deg, etc
--psi_step (OLD) : Angular sampling (before
oversampling) for the in-plane angle (default=10deg for
2D, hp sampling for 3D)
--offset_range (OLD) : Search range for origin offsets (in
pixels)
--offset_step (OLD) : Sampling rate for origin offsets (in
pixels)
--auto_local_healpix_order (OLD) : Minimum healpix order (before
oversampling) from which auto-refine procedure will use local searches
--sigma_ang (OLD) : Stddev on all three Euler angles for
local angular searches (of +/- 3 stddev)
--sigma_rot (OLD) : Stddev on the first Euler angle for
local angular searches (of +/- 3 stddev)
--sigma_tilt (OLD) : Stddev on the first Euler angle for
local angular searches (of +/- 3 stddev)
--sigma_psi (OLD) : Stddev on the in-plane angle for
local angular searches (of +/- 3 stddev)
--sigma_off (OLD) : Stddev. on the translations
====== Corrections =====
--scale (OLD) : Switch on intensity-scale
corrections on image groups
--norm (OLD) : Switch on normalisation-error
correction
====== Computation =====
--j (1) : Number of threads to run in parallel
(only useful on multi-core machines)
--pool (OLD) : Number of images to be processed
together
--cpus_per_node (8) : Maximum number of models for which
the FT can be set simultaneously (decrease in case of
memory problems in this step)
--verb (1) : Verbosity (1=normal, 0=silent)
====== Expert options =====
--strict_highres_exp (OLD) : Resolution limit (in Angstrom) to
restrict probability calculations in the expectation step
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
Matteo Allegretti
PhD candidate
Max Planck Institut für Biophysik
Max-von-Laue-Straße 3
D-60438 Frankfurt am Main
Office: +49-69-6303-3015
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