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scipion-em / scipion-em-empiar

A Scipion plugin to make depositions to EMPIAR
GNU General Public License v3.0
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??? #22

Closed azazellochg closed 3 years ago

azazellochg commented 3 years ago

I dont understand what's the depositor protocol is doing.. I'm trying a simple test without actual deposition. I put input set only imported movies. I see in the logs:

Logging configured. STDOUT --> Runs/003808_EmpiarDepositor/logs/run.stdout , STDERR --> Runs/003808_EmpiarDepositor/logs/run.stderr
RUNNING PROTOCOL -----------------
Protocol starts
Hostname: hal.lmb.internal
PID: 2959955
pyworkflow: 3.0.16
plugin: empiar
plugin v: 3.0.6
currentDir: /cephfs/gsharov/ScipionUserData/projects/relion40_tutorial
workingDir: Runs/003808_EmpiarDepositor
runMode: Restart
          MPI: 1
      threads: 1
 Starting at step: 1
 Running steps 
STARTED: createDepositionStep, step 1, time 2021-08-10 13:59:58.239760
output key is outputMovies
 xmipp_transform_filter  -i Runs/000002_ProtImportMovies/extra/20170629_00021_frameImage.tiff -o Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage.tiff --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000002_ProtImportMovies/extra/20170629_00021_frameImage.tiff
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage.tiff
 xmipp_transform_filter  -i Runs/000002_ProtImportMovies/extra/20170629_00022_frameImage.tiff -o Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage.tiff --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000002_ProtImportMovies/extra/20170629_00022_frameImage.tiff
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage.tiff
 xmipp_transform_filter  -i Runs/000002_ProtImportMovies/extra/20170629_00023_frameImage.tiff -o Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage.tiff --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000002_ProtImportMovies/extra/20170629_00023_frameImage.tiff
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage.tiff
output key is outputMovies
 xmipp_transform_filter  -i Runs/000002_ProtImportMovies/extra/20170629_00021_frameImage.tiff -o Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage.tiff --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000002_ProtImportMovies/extra/20170629_00021_frameImage.tiff
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage.tiff
 xmipp_transform_filter  -i Runs/000002_ProtImportMovies/extra/20170629_00022_frameImage.tiff -o Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage.tiff --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000002_ProtImportMovies/extra/20170629_00022_frameImage.tiff
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage.tiff
 xmipp_transform_filter  -i Runs/000002_ProtImportMovies/extra/20170629_00023_frameImage.tiff -o Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage.tiff --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000002_ProtImportMovies/extra/20170629_00023_frameImage.tiff
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage.tiff
output key is outputMicrographsDoseWeighted
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00021_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00021_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage_aligned_mic_DW.mrc
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00022_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00022_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage_aligned_mic_DW.mrc
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00023_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00023_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage_aligned_mic_DW.mrc
output key is outputCTF
output key is outputCoordinates
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00021_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00021_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage_aligned_mic_DW.mrc
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00022_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00022_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage_aligned_mic_DW.mrc
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00023_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00023_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage_aligned_mic_DW.mrc
output key is outputCoordinates
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00021_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00021_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage_aligned_mic_DW.mrc
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00022_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00022_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage_aligned_mic_DW.mrc
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00023_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00023_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage_aligned_mic_DW.mrc
output key is boxsize
output key is outputParticles
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
output key is outputClasses
output key is outputParticles
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
output key is outputVolume
output key is outputParticles
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
output key is outputVolumeAligned
output key is outputVolumeSymmetrized
output key is outputClasses
output key is outputVolumes
output key is outputParticles
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000657_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
output key is outputRepresentatives
output key is outputCoordinates
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00021_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00021_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage_aligned_mic_DW.mrc
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00022_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00022_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00022_frameImage_aligned_mic_DW.mrc
 xmipp_transform_filter  -i Runs/000087_ProtRelionMotioncor/extra/20170629_00023_frameImage_aligned_mic_DW.mrc -o Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage_aligned_mic_DW.mrc --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000087_ProtRelionMotioncor/extra/20170629_00023_frameImage_aligned_mic_DW.mrc
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00023_frameImage_aligned_mic_DW.mrc
output key is outputParticles
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
output key is outputVol
output key is outputVolume
output key is outputParticles
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
 xmipp_transform_filter  -i Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs -o Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/001215_ProtRelionExtractParticles/extra/mic_000001.mrcs
Output File: Runs/003808_EmpiarDepositor/tmp/mic_000001.mrcs
output key is outputFSC
output key is outputMask
output key is outputClasses
output key is outputMovies
 xmipp_transform_filter  -i Runs/000002_ProtImportMovies/extra/20170629_00021_frameImage.tiff -o Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage.tiff --fourier low_pass 0.050000
Filter Band: Lowpass before 0.05
Filter Shape: Raised cosine with 0.02 raised frequencies
Input File: Runs/000002_ProtImportMovies/extra/20170629_00021_frameImage.tiff
Output File: Runs/003808_EmpiarDepositor/tmp/20170629_00021_frameImage.tiff

Why is it lowpass filtering movies? Why is it processing other protocols from my project?

sanlopez commented 3 years ago

@azazellochg, the protocol creates several items (in the "extra/images_representation" protocol folder) for representing each step from the analysis. In the case of micrographs, a low pass filtering is applied in order to improve the images quality, that is the reason you see these lines in the log.

azazellochg commented 3 years ago

Hi,

I understand. My question is why is it processing the whole project as I only intended to upload movies. Best regards, Grigory

Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: @.***

On Wed, Aug 18, 2021 at 4:51 PM Irene @.***> wrote:

@azazellochg https://github.com/azazellochg, the protocol creates several items (in the "extra/images_representation" protocol folder) for representing each step from the analysis. In the case of micrographs, a low pass filtering is applied in order to improve the images quality, that is the reason you see these lines in the log.

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sanlopez commented 3 years ago

Hi Grigory,

As I said, that is done in order to create image thumbnails for every step of the analysis (that ultimately would be used used in the web workflow viewer). Cheers, Irene