Import Result Group: Skip Importing Micrographs When Importing Particles

Import and Export
1

It seems I need give the raw image with the particle to import it to another instance.I can’t just import the particles from one cryosparc instance to another cryosparc instance

License is valid.

Running job on master node

[CPU: 96.1 MB]   Project P1 Job J13 Started

[CPU: 96.1 MB]   Master running v2.16.1-live_deeppick_privatebeta+200728, worker running v2.16.1-live_deeppick_privatebeta+200728

[CPU: 96.3 MB]   Running on lane default

[CPU: 96.3 MB]   Resources allocated: 

[CPU: 96.3 MB]     Worker:  localhost

[CPU: 96.3 MB]   --------------------------------------------------------------

[CPU: 96.3 MB]   Importing job module for job type import_result_group...

[CPU: 188.8 MB]  Job ready to run

[CPU: 188.8 MB]  ***************************************************************

[CPU: 188.8 MB]  Importing result group from /data/shuaishuai/P1/imports/jobs/P3_J283_particles/P3_J283_particles_exported.csg

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_11743_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_10725_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_12289_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_09866_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_10416_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_13532_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_11514_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_11324_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_09944_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_12066_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_11044_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_13408_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_11946_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_13415_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_11835_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_10668_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_13170_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_10536_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_12194_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_10706_SumCorr2.mrc

[CPU: 195.9 MB]  Unable to find /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_11307_SumCorr2.mrc
2

Hi,
maybe a stupid question, but can you do
ls -la /data/shuaishuai/P1/imports/jobs/P3_J283_particles/J280/imported/stack0910_11743_SumCorr2.mrc
?
If yes and the file is there, then it may be that the ownership is different from one instance to the other.
Cheers,
Juan

3

Hi,
Thanks for your reply.I know what you said.So I said I need give raw micrograh.I think it will be better when import can skip the raw micrograph.Because I just want to import particles image to a new instance.

4

You could softlink the data also to the new location… using ln -s.
But maybe it’s quite cumbersome if you don’t have lists.
I had a migration recently and most of the problems importing projects were not connected with where is the data but with who’s owning it. :weary:

5

hh,I know,my data is in another GPU workstation,so I still need to transport my raw micrograph from a GPU workstation to another GPU workstation.It is not very convinent.I just want to skip that step.Of course,It’s not a big problem.

6

Hi @wonderful,

To skip the importing of particle locations (the correspondance between the particles and their source micrographs), open up the .csg file you’re trying to import and delete the lines associated with location.
For example, if your .csg file looked like the following:

group:
  description: All particles that were processed, including alignments across all
    classes.
  name: particles
  title: All particles
  type: particle
results:
  alignments2D:
    metafile: '>P26_J31_particles_exported.cs'
    num_items: 1750
    type: particle.alignments2D
  blob:
    metafile: '>P26_J31_particles_exported.cs'
    num_items: 1750
    type: particle.blob
  ctf:
    metafile: '>P26_J31_particles_exported.cs'
    num_items: 1750
    type: particle.ctf
  location:
    metafile: '>P26_J31_particles_exported.cs'
    num_items: 1750
    type: particle.location
  pick_stats:
    metafile: '>P26_J31_particles_exported.cs'
    num_items: 1750
    type: particle.pick_stats
version: develop

You would remove the four lines:

location:
    metafile: '>P26_J31_particles_exported.cs'
    num_items: 1750
    type: particle.location

And import the .csg file again.

7

Hi @stephan,

Thanks for your reply,and I have removed the four lines.But I still have this problem.Is there other thing I need do?Looking forward your reply.Thanks very much.

shuaishuai

8

Hi @stephan,

I still meet a problem.When I change the .csg file as your advise,and I remove the field of location in .cs file.I can Import the particles successful.But when I using this particles to do 2D classification.It gives me a err “TypeError: object of type ‘NoneType’ has no len()”.Can you give me some advise about that?I am confused about that.

shuaishuai