Dear all,
i'm facing some problems while attempting to extract particles from a
tilted collection after local ctf estimation.
Here is what i've done.
I created a folder on the root of my relion pipeline directory named
"GCTF"
Inside this directory, i linked my .mrc files and their corresponding
coordinates _autopick.star.
I ran gctf per-particle local estimation from the shell using this
command :
/opt/Gctf_v1.18_b2/Gctf_v1.18_b2_sm61_cu8.0
in24981-8/raw/Images-Disc1/GridSquare_5312228/Data/*.mrc --do_EPA 1
--apix 0.83 --kV 300 --Cs 2.7 --do_local_refine 1 --do_validation 1
--boxsuffix _autopick.star
This is an example but in fact i have to launch this command many time
since i have multiple "GridSquare_531XXX folder. I just wanted to follow
the path i used when i import my movies at the beginning.
Anyway, it works well and i created .ctf ; .epa ; _EPA.log ; _gctf.log ;
_local.star and .pow files.
A file named micrographs_all_gctf.star was also created in the first
folder.
Then i import my _local.star coordinate inside Relion 3.1.
The main problem occurs during the extraction job.
I use as input the corrected_micrographs.star generated by MotionCorr
(containing .mrc files i linked for the local ctf estimation), and i
input the coordinate _local.star.
The first error is that relion can't find the coordinate (see below)
Warning: coordinate file
Import/job110/in24981-8/raw/Images-Disc1/GridSquare_5312561/Data/FoilHole_5353091_Data_5320469_5320471_20200208_100409_fractions_local.star
does not exist..
When i go through the Import/job110 directory, i can see the following
path :
GCTF/in24981-8/raw/Images-Disc1/GridSquare_XXX/Data/XXX_local.star.
My idea was to remove the "GCTF" directory in order to keep the
following path :
in24981-8/raw/Images-Disc1/GridSquare_XXX/Data/XXX_local.star in order
to help relion to find the correct path, where my _local.star files are.
But when i want to relaunch the extraction job this error occurs :
in: /home/install/code/relion-3.1/src/jaz/obs_model.cpp, line 730
ERROR:
=== Backtrace ===
/cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN11RelionErrorC1ERKSsS1_l+0x41)
[0x43d741]
/cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZNK16ObservationModel14getOpticsGroupERK13MetaDataTablel+0xef)
[0x47301f]
/cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x2c58)
[0x44a458]
/cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x5c3)
[0x44d353]
/cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN13Preprocessing19runExtractParticlesEv+0x2e6)
[0x44de76]
/cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN13Preprocessing3runEv+0x12)
[0x44e0f2]
/cm/shared/apps/relion-3.1-b/bin/relion_preprocess(main+0x3d) [0x41c48d]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2aaab74fb3d5]
/cm/shared/apps/relion-3.1-b/bin/relion_preprocess() [0x41cd1f]
==================
ERROR:
By the way, i tried so many combinaison, and it systematically return a
relion's problem, even if i import the micrographs_all_gctf.star.
Any help will be appreciated because i'm stuck through this problem...
Best regards
--
KEVIN MARTIN
PharmD-PhD student
Centre de biochimie structurale (CBS)
29, Rue de Navacelles
FR-34090 Montpellier
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