Hi,
I’m trying to run topaz train job and getting this error:
ValueError: All arrays must be of the same length
All processing was done in cryosparc.
Traceback (most recent call last):
[CPU: 244.6 MB Avail: 503.31 GB]
File “/programs/x86_64-linux/topaz/0.2.5_cu11/bin/topaz”, line 11, in
[CPU: 244.6 MB Avail: 503.31 GB]
load_entry_point(‘topaz-em==0.2.4’, ‘console_scripts’, ‘topaz’)()
[CPU: 244.6 MB Avail: 503.31 GB]
File “/programs/x86_64-linux/topaz/0.2.5_cu11/topaz_extlib/miniconda3-4.7.12.1-j4hb/lib/python3.7/site-packages/topaz/main.py”, line 148, in main
[CPU: 244.6 MB Avail: 503.31 GB]
args.func(args)
[CPU: 244.6 MB Avail: 503.31 GB]
File “/programs/x86_64-linux/topaz/0.2.5_cu11/topaz_extlib/miniconda3-4.7.12.1-j4hb/lib/python3.7/site-packages/topaz/commands/train_test_split.py”, line 128, in main
[CPU: 244.6 MB Avail: 503.31 GB]
image_list_train = pd.DataFrame({‘image_name’: image_names_train, ‘path’: paths_train})
[CPU: 244.6 MB Avail: 503.31 GB]
File “/programs/x86_64-linux/topaz/0.2.5_cu11/topaz_extlib/miniconda3-4.7.12.1-j4hb/lib/python3.7/site-packages/pandas/core/frame.py”, line 614, in init
[CPU: 244.6 MB Avail: 503.31 GB]
mgr = dict_to_mgr(data, index, columns, dtype=dtype, copy=copy, typ=manager)
[CPU: 244.6 MB Avail: 503.31 GB]
File “/programs/x86_64-linux/topaz/0.2.5_cu11/topaz_extlib/miniconda3-4.7.12.1-j4hb/lib/python3.7/site-packages/pandas/core/internals/construction.py”, line 465, in dict_to_mgr
[CPU: 244.6 MB Avail: 503.31 GB]
arrays, data_names, index, columns, dtype=dtype, typ=typ, consolidate=copy
[CPU: 244.6 MB Avail: 503.31 GB]
File “/programs/x86_64-linux/topaz/0.2.5_cu11/topaz_extlib/miniconda3-4.7.12.1-j4hb/lib/python3.7/site-packages/pandas/core/internals/construction.py”, line 119, in arrays_to_mgr
[CPU: 244.6 MB Avail: 503.31 GB]
index = _extract_index(arrays)
[CPU: 244.6 MB Avail: 503.31 GB]
File “/programs/x86_64-linux/topaz/0.2.5_cu11/topaz_extlib/miniconda3-4.7.12.1-j4hb/lib/python3.7/site-packages/pandas/core/internals/construction.py”, line 635, in _extract_index
[CPU: 244.6 MB Avail: 503.31 GB]
raise ValueError(“All arrays must be of the same length”)
[CPU: 244.6 MB Avail: 503.31 GB]
ValueError: All arrays must be of the same length
[CPU: 244.6 MB Avail: 503.31 GB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 96, in cryosparc_compute.run.main
File “/data2/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py”, line 307, in run_topaz_wrapper_train
utils.run_process(split_command)
File “/data2/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/topaz_utils.py”, line 98, in run_process
assert process.returncode == 0, f"Subprocess exited with status {process.returncode} ({str_command})"
AssertionError: Subprocess exited with status 1 (/programs/x86_64-linux/topaz/0.2.5_cu11/bin.capsules/topaz train_test_split --number 1183 --seed 1892525643 --image-dir /data3/P22/J282/preprocessed /data3/P22/J282/topaz_particles_processed.txt)