rdrighetto
commented
4 years ago Dear Ethan,
The "No handlers could be found for logger "mrcz.test_mrcz" message is just a warning, not an error. It can be safely ignored. But this "then: then/endif not found." error is indeed something we have to look into. Some questions:
1) Did you update FOCUS in between the different runs of particle picking? If yes, some bug could have been introduced. 2) How many "more images" did you include in your second run with 8 threads? And were you outputting the new picked particles into the same directory as before (the default is SPR/) \, or a different one? If the same, that could lead to some unexpected errors. 3) Are you splitting your particle stacks per-crystal or per-particle? There's an option for that. If you are picking particles from a single 2D crystal image you cannot split per-crystal, because you have only one.
Hope this helps and thanks for using FOCUS!
-- Ricardo Diogo Righetto
Em sex, 20 de set de 2019 às 05:09, EthanJUCB notifications@github.com escreveu:
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 = name@provider.com 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.#######################
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EthanJUCB
acdrennan
arndtbill1
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 = name@provider.com 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
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...