Bug #7282
closedappion CTFFIND error
0%
Description
I am getting this error past two weeks when I try to do CTF estimation through appion. Please see the attached screenshot
Files
Updated by Anchi Cheng over 5 years ago
- Status changed from New to Assigned
- Assignee set to Venkata Dandey
Have you ever run ctffind4 through appion at 3 Å pixel successful before ? The error occus while it is making the evaluation plots. I wonder if it is ever done at such large pixel size before.
Updated by Anchi Cheng over 5 years ago
- Assignee changed from Venkata Dandey to Shaker Krit
Please test with these python commands on node-48 with appion environment.
You can find '19apr18d_07gr_03sq_02hl_02en-pow_avrot.txt' in Venkat's rundir shown in his screenshot.
from appionlib.apCtf import ctffind4AvgRotPlot avgrotfile = '19apr18d_07gr_03sq_02hl_02en-pow_avrot.txt' outputpng = ctffind4AvgRotPlot.createPlot(avgrotfile)
This may be specific to the node he ran from. I was able to run it on node-39
The full appion command to test on the single image is
/opt/myamisnap/bin/appion ctffind4.py --ampcontrast=0.07 --fieldsize=1024 --resmin=50 --resmax=4 --defstep=0.1 --numstep=25 --dast=0.05 --min_phase_shift=10 --max_phase_shift=170 --phase_search_step=10 --num_frame_avg=7 --runname=ctffind4run2anchi --rundir=/gpfs/appion/acheng/19apr18d/ctf/ctffind4run2anchi --commit --projectid=63 --session=19apr18d --no-wait --no-continue --bestdb --expid=8911 --jobtype=ctfestimate --mrclist=19apr18d_gr_00007gr_00003sq_v02_00002hl_00002en.mrc
You must change rundir to be a directory that you have permission to write to, though.
Updated by Sargis Dallakyan over 5 years ago
I have been asking users to do `rm -rf ~/.matplotlib` in #4583, #3749 and elsewhere. I've decided to do this in the code instead. I'm running the same job now as vdandey and it seems to be working.
Updated by Anchi Cheng over 5 years ago
- Status changed from Assigned to Closed
- Assignee changed from Shaker Krit to Anchi Cheng
Thanks, Sargis.