Hello,
I tried several different workflows for Topaz Train, but they all failed. Did anyone ever stumbled upon this? Or does anyone know how to work around this?
Thank you,
Trial 1: Blob Picker → Inspect Picks → Extract Micrographs → 2D Classification → Select 2D Classes → Topaz Train
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Inputs to Topaz Train: Mics from Inspect Picks and ptcls from 2D.
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Result: Failed.
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Topaz executable:
/home/cryosparcuser/.conda/envs/topaz/bin/topaz
Trial 2: Inputs to Topaz Train: Mics from Extract Micrographs and ptcls from 2D Classes.
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Result: Failed.
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Topaz executable (I reinstalled Topaz again):
/home/cryosparcuser/topaz.sh
Trial 3: Inputs to Topaz Train: Both Mics and ptcls from Extract Micrographs.
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Result: Failed.
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The error message is as below:
\[CPU: 724.5 MB Avail: 499.77 GB\]
WARNING: no micrograph found matching image name "004206278573885948794_m26jul01d_NY1626_g3_00007GrK3_00072sq_v02_00005hl_00014enn.frames_patch_aligned_doseweighted". Skipping it.
\[CPU: 724.5 MB Avail: 499.77 GB\]
WARNING: no micrograph found matching image name "004094380918364751086_m26jul01d_NY1626_g3_00028GrK3_00046sq_v02_00004hl_00017enn.frames_patch_aligned_doseweighted". Skipping it.
\[CPU: 724.5 MB Avail: 499.77 GB\]
WARNING: no micrograph found matching image name "016343720720140038759_m26jul01d_NY1626_g3_00022GrK3_00047sq_v03_00003hl_00068enn.frames_patch_aligned_doseweighted". Skipping it.
\[CPU: 724.5 MB Avail: 499.77 GB\]
WARNING: no micrograph found matching image name "015512745986933156503_m26jul01d_NY1626_g3_00022GrK3_00047sq_v02_00002hl_v01_00035enn.frames_patch_aligned_doseweighted". Skipping it.
\[CPU: 724.5 MB Avail: 499.77 GB\]
Traceback (most recent call last):
\[CPU: 724.5 MB Avail: 499.77 GB\]
File "/home/cryosparcuser/miniforge3/envs/topaz/bin/topaz", line 33, in <module>
\[CPU: 724.5 MB Avail: 499.77 GB\]
sys.exit(load_entry_point('topaz-em==0.2.5', 'console_scripts', 'topaz')())
\[CPU: 724.5 MB Avail: 499.77 GB\]
File "/home/cryosparcuser/miniforge3/envs/topaz/lib/python3.6/site-packages/topaz/main.py", line 148, in main
\[CPU: 724.5 MB Avail: 499.77 GB\]
args.func(args)
\[CPU: 724.5 MB Avail: 499.77 GB\]
File "/home/cryosparcuser/miniforge3/envs/topaz/lib/python3.6/site-packages/topaz/commands/train_test_split.py", line 128, in main
\[CPU: 724.5 MB Avail: 499.77 GB\]
image_list_train = pd.DataFrame({'image_name': image_names_train, 'path': paths_train})
\[CPU: 724.5 MB Avail: 499.77 GB\]
File "/home/cryosparcuser/miniforge3/envs/topaz/lib/python3.6/site-packages/pandas/core/frame.py", line 468, in \__init_\_
\[CPU: 724.5 MB Avail: 499.77 GB\]
mgr = init_dict(data, index, columns, dtype=dtype)
\[CPU: 724.5 MB Avail: 499.77 GB\]
File "/home/cryosparcuser/miniforge3/envs/topaz/lib/python3.6/site-packages/pandas/core/internals/construction.py", line 283, in init_dict
\[CPU: 724.5 MB Avail: 499.77 GB\]
return arrays_to_mgr(arrays, data_names, index, columns, dtype=dtype)
\[CPU: 724.5 MB Avail: 499.77 GB\]
File "/home/cryosparcuser/miniforge3/envs/topaz/lib/python3.6/site-packages/pandas/core/internals/construction.py", line 78, in arrays_to_mgr
\[CPU: 724.5 MB Avail: 499.77 GB\]
index = extract_index(arrays)
\[CPU: 724.5 MB Avail: 499.77 GB\]
File "/home/cryosparcuser/miniforge3/envs/topaz/lib/python3.6/site-packages/pandas/core/internals/construction.py", line 397, in extract_index
\[CPU: 724.5 MB Avail: 499.77 GB\]
raise ValueError("arrays must all be same length")
\[CPU: 724.5 MB Avail: 499.77 GB\]
ValueError: arrays must all be same length
\[CPU: 724.5 MB Avail: 499.77 GB\]
**Traceback (most recent call last):
File "cryosparc_master/cryosparc_compute/run.py", line 116, in cryosparc_master.cryosparc_compute.run.main
File "/home/cryosparcuser/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py", line 332, in run_topaz_wrapper_train
utils.run_process(split_command)
File "/home/cryosparcuser/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/cryosparcuser/topaz.sh train_test_split --number 7475 --seed 1430494252 --image-dir /data/CS/20260701d_XXXXXX/CS-XXXXXX-J13/preprocessed /data/CS/20260701d_XXXXXX/CS-XXXXXX/J13/topaz_particles_processed.txt)**