Hi Xue,
How many lines does the file 2mics_ctf.starhave? and the file
2D_10classes.star? (Just to rule out something trivial)
Then, does the job go much faster if you give --min_distance 500?
Or does it go much faster if you do not give --write_fom_maps? or
--max_stddev_noise 1.1?
best,
Sjors
On 02/01/2017 11:26 AM, X.Y. Pei wrote:
> some correction on my previous message:
> one image took 44.74 hour for auto-picking,
> two images took 89.48 hour for auto-picking.
> MPI=1
> RAM=64Gb
> around 600 particles pre image
> xue
> On 2017-02-01 11:22, X.Y. Pei wrote:
>> Dear CryoEM community:
>> I have a job on the cluster with MPI=1, 64Gb RAM for 44.7 hour, auto
>> picking from two images (around 600 particles per image) in order to
>> optimize threshold and Dmin took 89.3hour. Here is my setting:
>>
>> application='`which relion_autopick` --i 2mics_ctf.star --o
>> 2mics240A140pi_autpick1 --particle_diameter 240 --angpix 1.77 --ref
>> 2D_10classes.star --invert --ctf --ang 5 --lowpass 20
>> --write_fom_maps --threshold 0.6 --min_distance 150
>> --max_stddev_noise 1.1 '
>>
>> I could not work out what is wrong in the job. Could any one please
>> give some comments on it?
>>
>> Much appreciate with your opinion.
>>
>> Xue
--
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
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