Too many arguments

[alexander-a-mestre]

Dear Focus-Team,

Our group is trying to use Focus to process 2D crystals. Currently, we are struggling to run the program “import movie from digitial micrograph”. Each time we attempt to import the movie we get the error message that there are too many arguments.

We have our Project directory set up as follows:

• Project_Directory/raw/movie01

We imported the raw gain-corrected mrc movies into Focus.

After selecting the movie from the library we to run the "Import Movie from Digitial Micrograph" program.

Our values are as follows Image Number: 0000000001 Comment: - Magnification: 40159.674 Pixel Size: 5 Calculate Pixel Size From magnification: yes Pixel Size on Sample Level: 1.24503 Use Pixel Size on header: yes Original Pixel Size on Sample Level: 1.24503 Crop Histogram: yes Crop_histogram_stdev:4 Original Filename: -

Name of rawstack: movie01.mrc Original name of raw stack: Project_Directory/raw/movie01.mrc Name of gain corrected raw stack: raw_gaincorrectedstack SerialEM applied conversion Factor:1 SerialEM default conversion factor: 12

Binning of this image before motioncor2: 2= bin by a factor of 2 Binning target pixel size: 1

Source of information about frame dose: 1= use electron counts in image Manually defined frame image dose: . Factor to increase the automatically determined electron dose: 1.3 Frame Image dose: ScriptWillPutNumberHere Frame Sample Dose: ScriptWillPutNumberHere Total Sample Dose: ScriptWillPutNumberHere CS:2 HT voltage: 300

How do we troubleshoot the “too many arguments” error message?

Best, Alex

[rdrighetto]

Hi Alexander,

It is not clear to me at what stage does the message "too many arguments" appear. If you set the verbosity of the FOCUS output to maximum and double-click it, it will open in a separate window where you can save or copy-paste the full output. Could you please send us that? Thanks.

[alexander-a-mestre]

Hi Sorry for the delayed reply.

The project directory had the test gain corrected movie in it.

The error message is shown below:

##################################import_DM###################################

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

Parameters requested by the Script

############################################ tempkeep = n imagename = 5cisp020movie nonmaskimagename = ScriptWillPutNameHere crop_histogram = y crop_histogram_stdev = 4.0 movie_stackname = 5cisp020movie import_rawstack = 5cisp020movie.mrc import_rawstack_type = 1 import_gainref = import_gainref_original = import_defects = import_defects_original = raw_gaincorrectedstack = 5cisp020movie magnification = 40159.674 stepdigitizer = 5.0 calc_from_sample_pixel = y sample_pixel = 1.24503 take_header_orig_sample_pixel = y orig_sample_pixel = 1.24503 movie_imagenumber_total = import_bin = 2 import_bin_target = 1.000 import_rawstack_original = /exports/people/ungerlab/aam1730/thirdattemptatfocus/5cisp020movie.mrcs serialem_factor = 1 serialem_default_factor = 12 import_original_time = 1537915383000 frame_image_dose_source = 1 frame_image_dose_factor = 1.3 frame_image_dose_manually = . movie_image_dose_source = 0 movie_image_dose_factor = 1.3 movie_image_dose_manually = 80.0 cs = 2 kv = 300.0 defocus_phase_shift_doit = - thread_number = 12 export_basedir = ../../EXPORT export_rawstack_subdir = raw

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

Parameters from the Preferences settings

############################################ app_python = /usr/bin/python app_cadaver = /usr/bin/cadaver app_anaconda = /usr/bin/python dir_ccp4 = /opt/ccp4-7.0-x64 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 = /opt/motioncor2/x64/MotionCor2 app_gctf = /usr/local/cina/Gctf/0.50_cuda7.5/bin/gctf app_ctffind = /usr/local/cina/ctffind/ctffind-4.1.4/ctffind app_gautomatch = /opt/gautomatch/x64/Gautomatch_v0.56/bin/gautomatch dir_eman2 = /opt/eman2/2.12/x64/EMAN2 dir_imod = /opt/imod/x64/imod_4.9.9 dir_frealign = /opt/frealign/frealign_v9.11 dir_relion = /usr/local/relion Default_CS = 2 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 = n MotionCor2_alone = y

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

Now the remainder of the original script:

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

++++++++++++++++++++++++++++++++ Initializing script environment ++++++++++++++++++++++++++++++++ date = Wed Oct 3 15:55:17 CDT 2018 system = Linux bin_2dx = /exports/Linux/opt/focus-git/x64/focus-20180925-1/kernel/mrc/bin proc_2dx = /exports/Linux/opt/focus-git/x64/focus-20180925-1/scripts/proc ==== dir_eman2 = /opt/eman2/2.12/x64/EMAN2 ============================================================================================================================================================ ==== app_python = /usr/bin/python ===================================================================================================================================================================== ==== app_anaconda = /usr/bin/python =================================================================================================================================================================== ==== dir_frealign = /opt/frealign/frealign_v9.11 ====================================================================================================================================================== ==== dir_relion = /usr/local/relion =================================================================================================================================================================== Raw movie as gain-corrected stack is present as MRCS file. Gain-corrected stack is 5cisp020movie.mrcs Image has size 3710, which is small enough, no binning done.

source: Too many arguments. ::#############################import_DM finished.##############################

[alexander-a-mestre]

Any advice you have would be greatly appreciated.

[rdrighetto]

Hi,

Sorry for the delay. This happens because in your system csh is not tcsh. In modern Linux distros csh is just a symlink to tcsh. For more details and solution, please refer to our issue #171

Hope this helps.