2d-classification fail, particle.blob error V2


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?



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?



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
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:



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



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:



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