problems with particle extraction from 2d crystal

[EthanJUCB]

Hi, I have some problems during particle extraction. In the beginning, I was able to extract particles from several images with the error" No handlers could be found for logger "mrcz.test_mrcz" . I successfully had phase flipped stacks for crystal averages.

Then I tried to include more images using 8 threads. Somehow, only 1 thread was running according to system monitor and scripts stopped after extracting particles from up to 4 images no matter how many image I selected.

After that, I had the worst one, script completely stopped extracting even for a single image. It now shows similar error"No handlers could be found for logger "mrcz.test_mrcz" but with additional message " then: then/endif not found."

I have no idea how to fix it now. Please see attached log. Many thanks.

Best Xi

###########################PickExportParticleStack############################

############################################

Parameters requested by the Script

############################################ thread_number = 8 scriptname = spr_sample_pixel = 0.5568 spr_doresample = n spr_resmin = 100.0 spr_resmax = 10.0 spr_phaseshift = 0.0,180.0 spr_boxsize = 200 spr_sigcc = 0.3 spr_invertcontrast = y spr_normalizebox = y spr_calculatedefocustilted = y spr_savephaseflipped = y spr_savectfmultiplied = n spr_savewienerfiltered = n spr_wienerconstant = 0.4 spr_sigmanorm = 1.0 spr_radnorm = 0.90 spr_whichtiltgeometry = Defocus spr_whichctf = Particle spr_whichhalfset = particle-based spr_savepickfig = y cs = 2.6 kv = 300 sample_pixel = 0.5568 phacon = 0.995 magnification = 89798.9 use_masked_image = n spr_ignore_lat2 = y spr_ignore_c1 = y spr_createstarfile = y spr_dir = SPR spr_imgs_dir = spr_mergefile = spr_stacks_dir = spr_picking_dir = spr_stack_rootname =

############################################

Parameters from the Preferences settings

############################################ app_python = /usr/bin/python2.7 app_cadaver = /usr/bin/cadaver app_anaconda = /usr/bin/python2.7 dir_ccp4 = /usr/local/ccp4-7.0 app_gawk = /usr/bin/gawk cuda_library = /usr/local/cuda/lib64 app_unblur = /usr/local/cina/unblur/unblur_1.0.2/bin/unblur_openmp_7_17_15.exe app_motioncor2 = /home/xijiang/Downloads/Motioncor2/MotionCor2-01-30-2017 app_gctf = /home/xijiang/Downloads/Gctf_v1.06/bin/Gctf-v1.06_sm_30_cu8.0_x86_64 app_ctffind = /home/xijiang/Downloads/CTFFIND4/bin/ctffind app_gautomatch = /home/xijiang/Downloads/Gautomatch_v0.53/bin/Gautomatch-v0.53_sm_20_cu8.0_x86_64 dir_eman2 = /usr/local/EMAN2/bin dir_imod = /usr/local/IMOD dir_frealign = /home/xijiang/Downloads/frealign-2dx-master/bin dir_relion = /usr/local/relion3 Microscope_Name = CryoEM Default_CS = 2.6 Default_KV = 300.0 Default_phase_shift_doit = n status_folder_update = n status_folder = none status_microscope = Titan status_refresh_rate = 0 status_webdav = http://my.server.com/files website_blur_doit = y website_blurkernel = 7 SCRATCH_DISK = . FAST_DISK = . GPU_how_many = 1 GPU_to_use = 0 GPU_cycle = y MotionCor2_alone = y notify_email_admin = y notify_email_admin_adress = [email protected] notify_last_minutes = 15 notify_delay_minutes = 60 notify_lastnumber = 50 notify_limit_mild = 30 notify_limit_severe = 15 flag_isdark_threshold = 0.1 flag_hasstripe_threshold = 38.0 flag_hastoohighdefocus_threshold = 7.0 flag_hastoolowdefocus_threshold = 0.2 flag_icinesstoohigh_threshold = 1.6 flag_drifttoohigh_threshold = 50.0 flag_astigmatismtoohigh_threshold = 0.03 flag_ctfresolutiontoobad_threshold = 8.0

#############################################

Now the remainder of the original script:

#############################################

++++++++++++++++++++++++++++++++ Initializing script environment ++++++++++++++++++++++++++++++++

Running the following shell: version tcsh 6.18.01 (Astron) 2012-02-14 (x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,color,filec

date = Thu Sep 19 20:01:59 PDT 2019 system = Linux bin_2dx = /opt/focus/kernel/mrc/bin proc_2dx = /opt/focus/scripts/proc ==== dir_eman2 = /usr/local/EMAN2/bin ================================================================================================================================================================= ==== app_python = /usr/bin/python2.7 ================================================================================================================================================================== ==== app_anaconda = /usr/bin/python2.7 ================================================================================================================================================================ ==== dir_frealign = /home/xijiang/Downloads/frealign-2dx-master/bin =================================================================================================================================== ==== dir_relion = /usr/local/relion3 ================================================================================================================================================================== ==== dir_ccp4 = /usr/local/ccp4-7.0 =================================================================================================================================================================== Finding CSH setup script from CCP4 installation.. Sourcing /usr/local/ccp4-7.0/bin/ccp4.setup-csh Finished with /usr/local/ccp4-7.0/bin/ccp4.setup-csh Will use 1 threads for optimal load balancing. [1] 18154 No handlers could be found for logger "mrcz.test_mrcz" Job 1/1 picking particles from micrographs 1 to 1...

[1] Done /usr/bin/python2.7 /opt/focus/scripts/proc/SPR_ExtractParticles.py ../ SPR/2dx_merge_dirfile-unique.dat SPR/picking/ SPR/stacks/ particles 200 0.0,180.0 0.5568 300 2.6 0.995 89798.9 0.3 y y y y n n 0.4 1.0 0.90 Defocus Particle y n n 1 1 Now organizing and converting partial stack(s) to single .mrcs and .par files... then: then/endif not found. ::######################PickExportParticleStack finished.#######################