Unable to find .star file for 'import ptcl stack' job on v4.6.0

Import and Export
1

Hello,
I finished processing a dataset on Cluster 1 (Project P1). Afterward, I moved the entire processed workflow to Cluster 2 and archived P1 on the CryoSPARC UI. Now, I want to import the “J22 - Extraction from Micrographs” job from Cluster 2 P1.

To do this, I copied the complete J22 folder from Cluster 2 back to Cluster 1, creating a new folder and a new project (P2) in Cluster 1. Now, I want to start with an “Import Particle Stack” job in P2, and I need to set the paths for the ‘particle meta path’ and ‘particle data path’.

From my understanding:

  1. The “particle meta path” should point to a .star file. However, I am unsure where to find this file, as I only see the following files in the J22 folder:
    J22_micrographs.csg
    J22_passthrough_micrographs.cs
    J22_passthrough_particles.cs
    extract
    gridfs_data
    job.log
    J22_particles.csg
    J22_passthrough_micrographs_incomplete.cs
    events.bson
    extracted_particles.cs
    job.json
    picked_micrographs.cs

  2. For the “particle data path”, I believe I should use the .mrc files found in the “extract” folder. Is that correct?

I came across a few similar discussions but I am not able to find my .star file. Any help would really save me a great amount of time, and would be really appreciated!

Thanks,
Abhipsa

2

Hey everyone,

I managed to convert the .cs file to a .star file, but I encountered a couple of issues:

  1. During the conversion process, I received the following message. However, the output file was still generated successfully.

(pyem_env) abhipshaa@Abhipsas-MacBook-Air-2 pyem % csparc2star.py /Users/abhipshaa/Desktop/extracted_particles.cs /Users/abhipshaa/Desktop/extracted_particles_032625.star
Defocus values not found

  1. After running the “import particle stack” job, it completed, but I am seeing some warnings. (See below).

How should I handle these warnings? Can I safely ignore them and proceed with downstream jobs or I need to address these warnings? Has anyone dealt with similar issues before?

Thanks,
-Abhipsa

[CPU: 262.4 MB Avail: 475.70 GB]

Job ready to run
[CPU: 262.4 MB Avail: 475.70 GB]

[CPU: 262.4 MB Avail: 475.70 GB]

Importing particles from /XXXXXXXXXX/extracted_particles_032625.star

[CPU: 262.8 MB Avail: 475.70 GB]

File extension is star
[CPU: 262.8 MB Avail: 475.70 GB]

Importing star file.
[CPU: 531.9 MB Avail: 475.44 GB]

[CPU: 531.9 MB Avail: 475.44 GB]

Loaded star file with 395832 items
[CPU: 531.9 MB Avail: 475.44 GB]

Fields loaded from star file: [‘rlnImagePixelSize’, ‘rlnOpticsGroup’, ‘rlnImageSize’, ‘rlnImageDimensionality’, ‘rlnImageName’, ‘rlnMicrographName’, ‘rlnCoordinateX’, ‘rlnCoordinateY’, ‘rlnAngleRot’, ‘rlnAngleTilt’, ‘rlnAnglePsi’, ‘rlnOriginXAngst’, ‘rlnOriginYAngst’, ‘rlnPhaseShift’, ‘rlnRandomSubset’, ‘rlnClassNumber’]
[CPU: 531.9 MB Avail: 475.44 GB]

[CPU: 531.9 MB Avail: 475.44 GB]

Reading particle data locations…
[CPU: 531.9 MB Avail: 475.44 GB]

Reading rlnImageName to get indices and paths…
[CPU: 689.5 MB Avail: 475.31 GB]

Warning: Parameter particle_blob_path was set, which overrides rlnImageName despite the latter being present in the input star file.
[CPU: 689.7 MB Avail: 475.31 GB]

Parameter particle_blob_path was set and is a directory, so will be used as the search base for finding referenced data paths in the star file.
[CPU: 689.7 MB Avail: 475.31 GB]

Searching for linked data files…
[CPU: 689.7 MB Avail: 475.29 GB]

Warning: The input star file does not contain rlnAmplitudeContrast, and parameter amp_contrast was not set. Defaulting to Amplitude Contrast of 0.07
[CPU: 689.7 MB Avail: 475.29 GB]

Warning: The input star file does not contain rlnDefocusU and rlnDefocusV. Output will not contain CTF parameters for particles.
[CPU: 689.7 MB Avail: 475.29 GB]

Warning: The input star file does not contain rlnDefocusAngle. Output will not contain CTF parameters for particles.
[CPU: 689.7 MB Avail: 475.29 GB]

Warning: No exposures were connected as inputs, so correspondences cannot be found, so output will not contain pick locations for particles.
[CPU: 689.7 MB Avail: 475.29 GB]

[CPU: 689.7 MB Avail: 475.29 GB]

Compiling particle pose information…
[CPU: 689.7 MB Avail: 475.29 GB]

Converting euler angles…
[CPU: 689.7 MB Avail: 475.29 GB]

Converting rlnOriginXAngst to pixels using parameter psize_A
[CPU: 689.9 MB Avail: 475.28 GB]

3

Just a heads-up: The procedure described may violate several principles of CryoSPARC data management if

  1. Cluster 1 and cluster 2 are not connected to the same CryoSPARC (master) instance: When moving a project from CryoSPARC instance A to CryoSPARC instance B, one should
    i. detach the project from instance A, only then
    ii. move the project directory to instance B
    iii. attach the project to instance B

    The CryoSPARC Archive Project action should be used only when there is a plan to unarchive the project on the same CryoSPARC instance and the contents of the project directory remain unchanged between archiving and unarchiving.

  2. and/or with

    moved the entire processed workflow

    you referred to moving (implicitly a sequence of 1. copying, then 2. deleting the source copy) the project directory. Please ensure a project is detached or archived, as appropriate (see above), before moving the project directory.

Now, I want to import the “J22 - Extraction from Micrographs” job from Cluster 2 P1.

If you are merely interested in using the outputs of J22 in the new P2 project on cluster 1, please explore this use case and let us know if you have any questions.