michelixtract problem

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Oda Toshiyuki

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Mar 16, 2019, 3:04:30 AM3/16/19
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Dear Neville,

   I tried to test michelixtract with a tif image and a reference hdf, but the program got stuck at 1% without giving any obvious errors.
Outputs are pasted below. Please let me know what is wrong. Thank you.

Best regards,

Toshiyuki Oda

-------------------------------------------------------
Toshiyuki Oda Ph.D.
Professor
Department of Anatomy and Structural Biology,
Graduate School of Medicine
University of Yamanashi
1110 Shimokato, Chuo, Yamanashi JAPAN 409-3898
Phone:+81-55-273-6743 email:to...@yamanashi.ac.jp
-------------------------------------------------------


===========

spring --version && springenv python -c 'import platform; print platform.platform()'
Spring environment loaded.
GUI from package Emspring-0.86.1661
Spring environment loaded.
Linux-3.10.0-957.5.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
 
Beginning of the program michelixtrace (Emspring v0.86.1661): Fri, 15 Mar 2019 09:22:09
####################################################################################################
INFO:oda:
############################################ INPUT ############################################
INFO:startlog:

INFO:startlog:The following input parameters have been received:
INFO:startlog:Micrographs                              = /oda1/oda/spring_test/tfc_18-2_0007_Jan18_12_13_44_noDW.mrc
INFO:startlog:Diagnostic plot pattern                  = test.pdf
INFO:startlog:Helix reference                          = /oda1/oda/spring_test/TFC_job305_run_class001_2d.hdf
INFO:startlog:Invert option                            = True
INFO:startlog:Estimated helix width in Angstrom        = 200
INFO:startlog:Pixel size in Angstrom                   = 1.358
INFO:startlog:Binning option                           = True
INFO:startlog:Binning factor                           = 4
INFO:startlog:Tile size power spectrum in Angstrom     = 500
INFO:startlog:Tile overlap in percent                  = 80
INFO:startlog:Alpha threshold cc-map                   = 0.001
INFO:startlog:Absolute threshold option cc-map         = False
INFO:startlog:Absolute threshold cc-map                = 0.2
INFO:startlog:Order fit                                = 2
INFO:startlog:Minimum and maximum helix length         = (500, 1500)
INFO:startlog:Pruning cutoff bending                   = 2.0
INFO:startlog:Box file coordinate step                 = 70.0
INFO:startlog:Compute performance score                = False
INFO:startlog:Parameter search option                  = False
INFO:startlog:Manually traced helix file               = mic.box
INFO:startlog:MPI option                               = True
INFO:startlog:Number of CPUs                           = 1
INFO:startlog:Temporary directory                      = /oda1/oda/spring_test/temp
INFO:startlog:
############################################ START ############################################
INFO:startlog:progress state: 1 %  [>                                        ]
INFO:oda:The following temporary directories were made:
rank_id  node_name      process_id  directory                                                   space_required
---------  -----------  ------------  ----------------------------------------------------------  ----------------
0  oda1                13567  /oda1/oda/spring_test/temp/oda-15_Mar_2019_09_22_09-13567/  1.00GB
INFO:CPU0:startup_scan_mpi_programs:

INFO:CPU0:startup_scan_mpi_programs:The following nodes will handle the following micrographs:
node_id  micrographs
---------  -----------------------------------------------------------
0  /oda1/oda/spring_test/tfc_18-2_0007_Jan18_12_13_44_noDW.mrc
INFO:oda:/net/beetle/home/app/spring_v0-86-1661/parts/openmpi/bin/mpirun -np 1 /net/beetle/home/app/spring_v0-86-1661/bin/springenv /net/beetle/home/app/spring_v0-86-1661/bin/python cleanup.py
logged on Fri, 15 Mar 2019 09:22:10

Carsten Sachse

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Mar 22, 2019, 5:24:10 AM3/22/19
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Dear Toshiyuki,

Sorry for the delayed response. Right now, the error message is not very telling. Could you save your parameters from the GUI in a text file and run the entire process from the command line using:
michelixtrace --f parameter file

and provide me with the output? The GUI seems to swallow some error messages. Thanks.

Best wishes,


Carsten

On Saturday, 16 March 2019 08:04:30 UTC+1, Oda Toshiyuki wrote:
Dear Neville,

   I tried to test michelixtract with a tif image and a reference hdf, but the program got stuck at 1% without giving any obvious errors.
Outputs are pasted below. Please let me know what is wrong. Thank you.

Best regards,

Toshiyuki Oda

-------------------------------------------------------
Toshiyuki Oda Ph.D.
Professor
Department of Anatomy and Structural Biology,
Graduate School of Medicine
University of Yamanashi
1110 Shimokato, Chuo, Yamanashi JAPAN 409-3898
Phone:+81-55-273-6743
-------------------------------------------------------

Oda Toshiyuki

unread,
Mar 22, 2019, 5:45:55 AM3/22/19
to emspring
Dear Carsten,

     The error was about wrong value of Tile size power spectrum.

====
ValueError: Chosen reference size (434 Angstrom) is smaller than specified tile size of 500 Angstrom. Please increase reference or decrease tile size.
====

I changed the value to 300 A, and now it's working. Thank you very much for the advice.

Best,

Toshiyuki

2019年3月22日金曜日 18時24分10秒 UTC+9 Carsten Sachse:
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