Topaz extraction -struct.error: unpack requires a buffer of 1024 bytes

Particle Picking
1

Dear colleagues,

Running the Topaz Extract I received the following error - struct.error: unpack requires a buffer of 1024 bytes

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “/home/cryosparc_user/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py”, line 1182, in run_topaz_wrapper_extract
utils.run_process(extract_command)
File “/home/cryosparc_user/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/topaz_utils.py”, line 99, in run_process
assert process.returncode == 0, f"Subprocess exited with status {process.returncode} ({str_command})"
AssertionError: Subprocess exited with status 1 (/home/cryosparc_user/.conda/envs/topaz/bin/topaz extract --radius 24 --threshold -6 --up-scale 9 --assignment-radius -1 --min-radius 5 --max-radius 100 --step-radius 5 --num-workers 16 --device 0 --model /data/dmitry/cryosparc/CS-cs-XXXX/J467/mod…)

Any ideas?

Thank you.

Kind regards,
Dmitry

2

@Dmitry Please can you post a log excerpt that shows

  • the lines leading up and including struct.error
  • the relative position of struct.error with respect to the Traceback you posted already
  • the lines between the struct.error and Traceback
1 Like
3

Hello @wtempel and all,

The issue seemed to be solved.
One has to be careful when using a big dataset with Topaz (about 20 000 images).
Splitting dataset on pieces (about 8000) with later on Topaz extraction fixed the error.

Thank you.

Kind regards,
Dmitry

1 Like