Hi,
I’m running into the same issue with topaz 0.2.5a. I just moved in a lab that handle their cluster via SBgrid. I don’t have any control of how topaz was installed, but what I know is it was not installed through conda.
What could I do to resolve the error ? (see below)
[CPU: 233.6 MB]
Starting Topaz process using version 0.2.5a...
[CPU: 233.6 MB]
Random seed used is 58879618
[CPU: 233.6 MB]
--------------------------------------------------------------
[CPU: 233.6 MB]
Starting preprocessing...
[CPU: 233.6 MB]
Starting micrograph preprocessing by running command /programs/x86_64-linux/system/sbgrid_bin/topaz preprocess --scale 4 --niters 200 --num-workers 8 -o /data/work/kmartin/cryosparc/CS-XX/J63/preprocessed [10 MICROGRAPH PATHS EXCLUDED FOR LEGIBILITY]
[CPU: 233.6 MB]
Preprocessing over 2 processes...
[CPU: 233.8 MB]
Inverting negative staining...
[CPU: 233.9 MB]
Inverting negative staining complete.
[CPU: 233.9 MB]
Micrograph preprocessing command complete.
[CPU: 233.9 MB]
Starting particle pick preprocessing by running command /programs/x86_64-linux/system/sbgrid_bin/topaz convert --down-scale 4 --threshold 0 -o /data/work/kmartin/cryosparc/CS-XX/J63/topaz_particles_processed.txt /data/work/kmartin/cryosparc/CS-XX/J63/topaz_particles_raw.txt
[CPU: 233.9 MB]
Particle pick preprocessing command complete.
[CPU: 233.9 MB]
Preprocessing done in 83.719s.
[CPU: 233.9 MB]
--------------------------------------------------------------
[CPU: 233.9 MB]
Starting train-test splitting...
[CPU: 233.9 MB]
Starting dataset splitting by running command /programs/x86_64-linux/system/sbgrid_bin/topaz train_test_split --number 2 --seed 58879618 --image-dir /data/work/kmartin/cryosparc/CS-XX/J63/preprocessed /data/work/kmartin/cryosparc/CS-XX/J63/topaz_particles_processed.txt
[CPU: 233.9 MB]
# splitting 10 micrographs with 2060 labeled particles into 8 train and 2 test micrographs
[CPU: 233.9 MB]
Traceback (most recent call last):
[CPU: 233.9 MB]
File "/programs/x86_64-linux/topaz/0.2.5_cu11.2/bin/topaz", line 33, in <module>
[CPU: 233.9 MB]
sys.exit(load_entry_point('topaz-em==0.2.5', 'console_scripts', 'topaz')())
[CPU: 233.9 MB]
File "/programs/x86_64-linux/topaz/0.2.5_cu11.2/lib/python3.9/site-packages/topaz/main.py", line 148, in main
[CPU: 233.9 MB]
args.func(args)
[CPU: 233.9 MB]
File "/programs/x86_64-linux/topaz/0.2.5_cu11.2/lib/python3.9/site-packages/topaz/commands/train_test_split.py", line 108, in main
[CPU: 233.9 MB]
targets_train = pd.concat(groups_train, 0)
[CPU: 233.9 MB]
TypeError: concat() takes 1 positional argument but 2 were given
[CPU: 233.9 MB]
Traceback (most recent call last):
File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
File "/net/cemaster/data/software/cryoSPARC/V2/cryosparc2_worker/cryosparc_compute/jobs/topaz/run_topaz.py", line 307, in run_topaz_wrapper_train
utils.run_process(split_command)
File "/net/cemaster/data/software/cryoSPARC/V2/cryosparc2_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/system/sbgrid_bin/topaz train_test_split --number 2 --seed 58879618 --image-dir /data/work/kmartin/cryosparc/CS-XX/J63/preprocessed /data/work/kmartin/cryosparc/CS-XX/J63/topaz_particles_processed.txt)
I’m totally lost. So far by using the conda environment I never had this kind of problem.
Any help will be welcomed…
Thank you all
Kevin