Hi everyone,
I recently downloaded and installed topaz as per the installation instructions on both CS and the Topaz Github, with no errors. However, when I run the topaz executable (tried both the actual executable file and a wrapper script) I get the following error:
Traceback (most recent call last):
** File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_master.cryosparc_compute.run.main**
** File “/costa/soft/cryosparc/cryosparc2_worker/cryosparc_compute/jobs/topaz/run_topaz.py”, line 308, in run_topaz_wrapper_train**
** utils.run_process(split_command)**
** File “/costa/soft/cryosparc/cryosparc2_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 (/costa/home/tgstudent2/.conda/envs/topaz/bin/topaz train_test_split --number 20 --seed 2062720999 --image-dir /costa/home/tgstudent2/xxx/CS-xxx/J45/preprocessed /costa/home/tgstudent2/xxx/CS-xxx/J45/topaz_particles_processed.txt)
I am using CS version v4.4.1, and Topaz 0.2.5a.
I imported a non-downscaled particle set (about 300k - from all mics) from relion into my workspace and imported CTF-corrected (which had gone through patch-motion correction prior) micrographs from another CS project (same dataset). I then use a subset of these micrographs (150 - output from template picker job) as the input micrographs for the topaz train job. The imported particle dataset was the input particles. Topaz initialises correctly and preprocesses the micrographs, then proceeds to this error.
I have tried testing with particles from 20 mics from a template picker job (both mics and associated picked particles were the inputs) and yet, the same error. Was wondering if anyone has any ideas?
Below is also the associated job.log file
topaz.run_topaz cryosparc_compute.jobs.jobregister
========= sending heartbeat at 2024-10-10 22:09:30.172156
========= sending heartbeat at 2024-10-10 22:09:40.195153
========= sending heartbeat at 2024-10-10 22:09:50.221205
========= sending heartbeat at 2024-10-10 22:10:00.313382
========= sending heartbeat at 2024-10-10 22:10:10.372173
========= sending heartbeat at 2024-10-10 22:10:20.444211
========= sending heartbeat at 2024-10-10 22:10:30.474250
****** handle exception rc**
/costa/soft/cryosparc/cryosparc2_worker/cryosparc_compute/jobs/motioncorrection/mic_utils.py:95: NumbaDeprecationWarning: The ‘nopython’ keyword argument was not supplied to the ‘numba.jit’ decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See Deprecation Notices — Numba 0+untagged.871.g53e976f.dirty documentation for details.
** @jit(nogil=True)**
/costa/soft/cryosparc/cryosparc2_worker/cryosparc_compute/micrographs.py:563: NumbaDeprecationWarning: The ‘nopython’ keyword argument was not supplied to the ‘numba.jit’ decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See Deprecation Notices — Numba 0+untagged.871.g53e976f.dirty documentation for details.
** def contrast_normalization(arr_bin, tile_size = 128):**
Traceback (most recent call last):
** File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_master.cryosparc_compute.run.main**
** File “/costa/soft/cryosparc/cryosparc2_worker/cryosparc_compute/jobs/topaz/run_topaz.py”, line 308, in run_topaz_wrapper_train**
** utils.run_process(split_command)**
** File “/costa/soft/cryosparc/cryosparc2_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 (/costa/home/tgstudent2/.conda/envs/topaz/bin/topaz train_test_split --number 20 --seed 2062720999 --image-dir /costa/home/tgstudent2/xxx/CS-xxx/J45/preprocessed /costa/home/tgstudent2/xxx/CS-xxx/J45/topaz_particles_processed.txt)
set status to failed
========= main process now complete at 2024-10-10 22:10:38.822699.
========= monitor process now complete at 2024-10-10 22:10:38.827956.