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-------------------------------------------------------
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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