2d-classification fail, particle.blob error V2

2D Classification
1

Hi,

I am trying to commence a 2D classification after having imported particles from a RELION project (.star file), the importation of the particles seems to work fine, but when I try to input them into the next part of the pipeline (2D classification) I get an error message I cannot make head-or-tails of as it gives an AssertionError I’ve not seen before:

Launching job on lane default target gerty5 …

License is valid.

Running job on master node hostname gerty5

Project P3 Job J7 Started

Master running v2.0.27, worker running v2.0.27

Running on lane default

Resources allocated:

Worker: gerty5

CPU : [0, 1]

GPU : [0]

RAM : [0, 1]

SSD : True

Importing job module for job type class_2D…

Job ready to run

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/class2D/run.py”, line 47, in cryosparc2_compute.jobs.class2D.run.run_class_2D
File “cryosparc2_compute/jobs/runcommon.py”, line 219, in load_input_group
assert is_connected, “Slot %s.%s must be connected!” % (input_group_name, slot[‘name’])
AssertionError: Slot particles.blob must be connected!

Have anyone else encountered this, if so, how did you solve it?

Cheers,

Jens

2

Looks like you haven’t dragged the particle stack onto the input - you need to drag and drop the particle stack output from the import job onto the particle input area of the 2D classification job - does the particle input show up correctly in the right side bar?

Cheers
Oli

3

Hi,

Yes I definitely added something to the input, however I’m beginning to suspect that this might be the source of the trouble :slight_smile: In order to get an output from the import particle stack I had to click in the “ignore raw data” button to not get this message:

Loaded 205856 particles.

Common fields:

      ctf/accel_kv :  set([200.0])

         ctf/cs_mm :  set([2.7])

  ctf/amp_contrast :  set([0.1])

      blob/psize_A :  set([1.54])

        blob/shape :  [1952539658 1952539658]

===========================================================

Making plots…

Traceback (most recent call last):
File “cryosparc2_master/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/imports/run.py”, line 288, in run_import_particles
dispparts.read_blobs(proj_dir_abs)
File “cryosparc2_compute/particles.py”, line 75, in read_blobs
dtypes[rel_path] = mrc.mrc_datatype_to_dtype(hdr[‘datatype’])
File “cryosparc2_compute/blobio/mrc.py”, line 42, in mrc_datatype_to_dtype
assert False,‘Unsupported MRC datatype: {0}’.format(datatype)
AssertionError: Unsupported MRC datatype: 1594499167

here’s the inputs for the 2d-classification job:

input.png2168×1189 259 KB

Cheers,

Jens

4

Well yeah, that won’t work - it doesn’t have any particles to work with if you ignore raw data… which doesn’t explain the initial error during import.

The blob/shape line during import should have the dimensions of the extracted particles in pixels - e.g. 400 400 for a box size of 400. 1952539658 seems rather too large :slight_smile:

I would double check your star file and maybe check an individual particle stack (e.g. using header from IMOD) to make sure nothing looks out of the ordinary

Cheers
OIi

5

Hi,

thanks for the answer. The solution was only link the .star file in the field called “particle meta path” and leave the “particle data path” as blank :slight_smile:

Cheers,

Jens

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