Unable to run topaz 3.7.0 on cryoSPARC v4.7.0

[CFDavidHou]

Dear topaz community,

I recently upgraded cryoSPARC from V4.6.0 to V4.7.0

However, I found that my topaz 2.5.0 does not using GPU.

Then I remove topaz from my miniconda3 and install topaz 3.7.0

I am doing a traning job on cryoSPARC below.

Now I got errors that 'topaz_particles_processed_train.txt' does not exist.

I looked into the folder and confirmed.

My Nvidia driver is 560 and CUDA is 12.6

Thank you!

CFD Hou

License is valid.

Launching job on lane default target 430benson ...

Running job on master node hostname 430benson

[CPU:   88.9 MB  Avail: 121.79 GB]
Job J85 Started

[CPU:   88.9 MB  Avail: 121.79 GB]
Master running v4.7.0, worker running v4.7.0
topaz_particles_processed_train.txt
[CPU:   89.2 MB  Avail: 121.77 GB]
Working in directory: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85

[CPU:   89.2 MB  Avail: 121.77 GB]
Running on lane default

[CPU:   89.2 MB  Avail: 121.77 GB]
Resources allocated: 

[CPU:   89.2 MB  Avail: 121.77 GB]
  Worker:  *****

[CPU:   89.2 MB  Avail: 121.77 GB]
  CPU   :  [0, 1, 2, 3, 4, 5, 6, 7]

[CPU:   89.2 MB  Avail: 121.77 GB]
  GPU   :  [0]

[CPU:   89.2 MB  Avail: 121.77 GB]
  RAM   :  [0]

[CPU:   89.2 MB  Avail: 121.77 GB]
  SSD   :  False

[CPU:   89.2 MB  Avail: 121.77 GB]
--------------------------------------------------------------

[CPU:   89.2 MB  Avail: 121.77 GB]
Importing job module for job type topaz_train...

[CPU:  253.4 MB  Avail: 121.59 GB]
Job ready to run

[CPU:  253.4 MB  Avail: 121.59 GB]
***************************************************************

[CPU:  253.4 MB  Avail: 121.59 GB]
Topaz is a particle detection tool created by Tristan Bepler and Alex J. Noble.
Citations:
- Bepler, T., Morin, A., Rapp, M. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat Methods 16, 1153-1160 (2019) doi:10.1038/s41592-019-0575-8
- Bepler, T., Noble, A.J., Berger, B. Topaz-Denoise: general deep denoising models for cryoEM. bioRxiv 838920 (2019) doi: https://doi.org/10.1101/838920

Structura Biotechnology Inc. and cryoSPARC do not license Topaz nor distribute Topaz binaries. Please ensure you have your own copy of Topaz licensed and installed under the terms of its GNU General Public License v3.0, available for review at: https://github.com/tbepler/topaz/blob/master/LICENSE.
***************************************************************


[CPU:  269.5 MB  Avail: 121.27 GB]
Starting Topaz process using version 0.3.7...

[CPU:  269.5 MB  Avail: 121.27 GB]
Random seed used is 679567019

[CPU:  269.5 MB  Avail: 121.27 GB]
--------------------------------------------------------------

[CPU:  269.5 MB  Avail: 121.27 GB]
Starting preprocessing...

430benso
[CPU:  269.5 MB  Avail: 121.27 GB]
Using a downsampling factor of 9

[CPU:  269.5 MB  Avail: 121.27 GB]
Starting micrograph preprocessing by running command /home/user/miniconda3/envs/topaz/bin/topaz preprocess --scale 9 --niters 200 --num-workers 4 -o /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed [35 MICROGRAPH PATHS EXCLUDED FOR LEGIBILITY]


[CPU:  269.5 MB  Avail: 121.27 GB]
Preprocessing over 2 processes...

[CPU:  269.9 MB  Avail: 119.59 GB]
Inverting negative staining...

[CPU:  269.9 MB  Avail: 119.59 GB]
Inverting negative staining complete.


[CPU:  269.9 MB  Avail: 119.59 GB]
Micrograph preprocessing command complete.


[CPU:  269.9 MB  Avail: 119.60 GB]
Starting particle pick preprocessing by running command /home/user/miniconda3/envs/topaz/bin/topaz convert --down-scale 9 --threshold 0 -o /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed.txt /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_raw.txt


[CPU:  269.9 MB  Avail: 119.80 GB]
Particle pick preprocessing command complete.


[CPU:  269.9 MB  Avail: 119.81 GB]
Preprocessing done in 12.961s.

[CPU:  269.9 MB  Avail: 119.81 GB]
--------------------------------------------------------------

[CPU:  269.9 MB  Avail: 119.81 GB]
Starting train-test splitting...


[CPU:  269.9 MB  Avail: 119.81 GB]
Starting dataset splitting by running command /home/user/miniconda3/envs/topaz/bin/topaz train_test_split --number 6 --seed 679567019 --image-dir /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed.txt


[CPU:  269.9 MB  Avail: 119.91 GB]
# splitting 34 micrographs with 503 labeled particles into 28 train and 6 test micrographs

[CPU:  269.9 MB  Avail: 119.91 GB]
# writing: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed/FoilHole_11755151_Data_11757238_1_20250412_232354_fractions_patch_aligned_doseweighted_train.txt

[CPU:  269.9 MB  Avail: 119.91 GB]
# writing: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed/FoilHole_11755151_Data_11757238_1_20250412_232354_fractions_patch_aligned_doseweighted_test.txt

[CPU:  269.9 MB  Avail: 119.91 GB]
# writing: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed/image_list_train.txt

[CPU:  269.9 MB  Avail: 119.91 GB]
# writing: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed/image_list_test.txt

[CPU:  269.9 MB  Avail: 120.27 GB]

Dataset splitting command complete.


[CPU:  269.9 MB  Avail: 120.27 GB]
Train-test splitting done in 3.464s.

[CPU:  269.9 MB  Avail: 120.27 GB]
--------------------------------------------------------------

[CPU:  269.9 MB  Avail: 120.27 GB]
Starting training...


[CPU:  269.9 MB  Avail: 120.27 GB]
Starting training by running command /home/user/miniconda3/envs/topaz/bin/topaz train --train-images /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/image_list_train.txt --train-targets /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed_train.txt --test-images /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/image_list_test.txt --test-targets /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed_test.txt --num-particles 100 --learning-rate 0.0002 --minibatch-size 128 --num-epochs 10 --method GE-binomial --slack -1 --autoencoder 0 --l2 0.0 --minibatch-balance 0.0625 --epoch-size 5000 --model resnet16 --units 32 --dropout 0.0 --bn on --unit-scaling 2 --ngf 32 --num-workers 4 --cross-validation-seed 679567019 --radius 3 --num-particles 100 --device 0 --no-pretrained --save-prefix=/mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/models/model -o /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/train_test_curve.txt


[CPU:  269.9 MB  Avail: 120.06 GB]
# Loading model: resnet16

[CPU:  269.9 MB  Avail: 120.06 GB]
# Model parameters: units=32, dropout=0.0, bn=on

[CPU:  269.9 MB  Avail: 120.06 GB]
# Receptive field: 91

[CPU:  269.9 MB  Avail: 120.06 GB]
# Using device=0 with cuda=True

[CPU:  269.9 MB  Avail: 120.06 GB]
# When using GPU to load data, we only load in this process. Setting num_workers = 0.
License is valid.

Launching job on lane default target ***** ...

Running job on master node hostname *****n

[CPU:   88.9 MB  Avail: 121.79 GB]
Job J85 Started

[CPU:   88.9 MB  Avail: 121.79 GB]
Master running v4.7.0, worker running v4.7.0

[CPU:   89.2 MB  Avail: 121.77 GB]
Working in directory: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85

[CPU:   89.2 MB  Avail: 121.77 GB]
Running on lane default

[CPU:   89.2 MB  Avail: 121.77 GB]
Resources allocated: 

[CPU:   89.2 MB  Avail: 121.77 GB]
  Worker:  *****n

[CPU:   89.2 MB  Avail: 121.77 GB]
  CPU   :  [0, 1, 2, 3, 4, 5, 6, 7]

[CPU:   89.2 MB  Avail: 121.77 GB]
  GPU   :  [0]

[CPU:   89.2 MB  Avail: 121.77 GB]
  RAM   :  [0]

[CPU:   89.2 MB  Avail: 121.77 GB]
  SSD   :  False

[CPU:   89.2 MB  Avail: 121.77 GB]
--------------------------------------------------------------

[CPU:   89.2 MB  Avail: 121.77 GB]
Importing job module for job type topaz_train...

[CPU:  253.4 MB  Avail: 121.59 GB]
Job ready to run

[CPU:  253.4 MB  Avail: 121.59 GB]
***************************************************************

[CPU:  253.4 MB  Avail: 121.59 GB]
Topaz is a particle detection tool created by Tristan Bepler and Alex J. Noble.
Citations:
- Bepler, T., Morin, A., Rapp, M. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat Methods 16, 1153-1160 (2019) doi:10.1038/s41592-019-0575-8
- Bepler, T., Noble, A.J., Berger, B. Topaz-Denoise: general deep denoising models for cryoEM. bioRxiv 838920 (2019) doi: https://doi.org/10.1101/838920

Structura Biotechnology Inc. and cryoSPARC do not license Topaz nor distribute Topaz binaries. Please ensure you have your own copy of Topaz licensed and installed under the terms of its GNU General Public License v3.0, available for review at: https://github.com/tbepler/topaz/blob/master/LICENSE.
***************************************************************


[CPU:  269.5 MB  Avail: 121.27 GB]
Starting Topaz process using version 0.3.7...

[CPU:  269.5 MB  Avail: 121.27 GB]
Random seed used is 679567019

[CPU:  269.5 MB  Avail: 121.27 GB]
--------------------------------------------------------------

[CPU:  269.5 MB  Avail: 121.27 GB]
Starting preprocessing...


[CPU:  269.5 MB  Avail: 121.27 GB]
Using a downsampling factor of 9

[CPU:  269.5 MB  Avail: 121.27 GB]
Starting micrograph preprocessing by running command /home/user/miniconda3/envs/topaz/bin/topaz preprocess --scale 9 --niters 200 --num-workers 4 -o /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed [35 MICROGRAPH PATHS EXCLUDED FOR LEGIBILITY]


[CPU:  269.5 MB  Avail: 121.27 GB]
Preprocessing over 2 processes...

[CPU:  269.9 MB  Avail: 119.59 GB]
Inverting negative staining...

[CPU:  269.9 MB  Avail: 119.59 GB]
Inverting negative staining complete.


[CPU:  269.9 MB  Avail: 119.59 GB]
Micrograph preprocessing command complete.


[CPU:  269.9 MB  Avail: 119.60 GB]
Starting particle pick preprocessing by running command /home/user/miniconda3/envs/topaz/bin/topaz convert --down-scale 9 --threshold 0 -o /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed.txt /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_raw.txt


[CPU:  269.9 MB  Avail: 119.80 GB]
Particle pick preprocessing command complete.


[CPU:  269.9 MB  Avail: 119.81 GB]
Preprocessing done in 12.961s.

[CPU:  269.9 MB  Avail: 119.81 GB]
--------------------------------------------------------------

[CPU:  269.9 MB  Avail: 119.81 GB]
Starting train-test splitting...


[CPU:  269.9 MB  Avail: 119.81 GB]
Starting dataset splitting by running command /home/user/miniconda3/envs/topaz/bin/topaz train_test_split --number 6 --seed 679567019 --image-dir /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed.txt


[CPU:  269.9 MB  Avail: 119.91 GB]
# splitting 34 micrographs with 503 labeled particles into 28 train and 6 test micrographs

[CPU:  269.9 MB  Avail: 119.91 GB]
# writing: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed/FoilHole_11755151_Data_11757238_1_20250412_232354_fractions_patch_aligned_doseweighted_train.txt

[CPU:  269.9 MB  Avail: 119.91 GB]
# writing: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed/FoilHole_11755151_Data_11757238_1_20250412_232354_fractions_patch_aligned_doseweighted_test.txt

[CPU:  269.9 MB  Avail: 119.91 GB]
# writing: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed/image_list_train.txt

[CPU:  269.9 MB  Avail: 119.91 GB]
# writing: /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/preprocessed/image_list_test.txt

[CPU:  269.9 MB  Avail: 120.27 GB]

Dataset splitting command complete.


[CPU:  269.9 MB  Avail: 120.27 GB]
Train-test splitting done in 3.464s.

[CPU:  269.9 MB  Avail: 120.27 GB]
--------------------------------------------------------------

[CPU:  269.9 MB  Avail: 120.27 GB]
Starting training...


[CPU:  269.9 MB  Avail: 120.27 GB]
Starting training by running command /home/user/miniconda3/envs/topaz/bin/topaz train --train-images /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/image_list_train.txt --train-targets /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed_train.txt --test-images /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/image_list_test.txt --test-targets /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed_test.txt --num-particles 100 --learning-rate 0.0002 --minibatch-size 128 --num-epochs 10 --method GE-binomial --slack -1 --autoencoder 0 --l2 0.0 --minibatch-balance 0.0625 --epoch-size 5000 --model resnet16 --units 32 --dropout 0.0 --bn on --unit-scaling 2 --ngf 32 --num-workers 4 --cross-validation-seed 679567019 --radius 3 --num-particles 100 --device 0 --no-pretrained --save-prefix=/mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/models/model -o /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/train_test_curve.txt


[CPU:  269.9 MB  Avail: 120.06 GB]
# Loading model: resnet16

[CPU:  269.9 MB  Avail: 120.06 GB]
# Model parameters: units=32, dropout=0.0, bn=on

[CPU:  269.9 MB  Avail: 120.06 GB]
# Receptive field: 91

[CPU:  269.9 MB  Avail: 120.06 GB]
# Using device=0 with cuda=True

[CPU:  269.9 MB  Avail: 120.06 GB]
# When using GPU to load data, we only load in this process. Setting num_workers = 0.

[CPU:  269.9 MB  Avail: 120.06 GB]
# Training...

[CPU:  269.9 MB  Avail: 120.06 GB]
# source	split	p_observed	num_positive_regions	total_regions

[CPU:  269.9 MB  Avail: 120.06 GB]
Traceback (most recent call last):

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/bin/topaz", line 33, in <module>

[CPU:  269.9 MB  Avail: 120.06 GB]
sys.exit(load_entry_point('topaz-em==0.3.7', 'console_scripts', 'topaz')())

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/main.py", line 148, in main

[CPU:  269.9 MB  Avail: 120.06 GB]
args.func(args)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/commands/train.py", line 140, in main

[CPU:  269.9 MB  Avail: 120.06 GB]
classifier = train_model(classifier, args.train_images, args.train_targets, args.test_images, args.test_targets,

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/training.py", line 607, in train_model

[CPU:  269.9 MB  Avail: 120.06 GB]
num_positive_regions, total_regions, num_images = report_data_stats(train_images_path, train_targets_path, test_images_path, test_targets_path,

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/training.py", line 284, in report_data_stats

[CPU:  269.9 MB  Avail: 120.06 GB]
train_targets = file_utils.read_coordinates(train_targets_path)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/utils/files.py", line 201, in read_coordinates

[CPU:  269.9 MB  Avail: 120.06 GB]
particles = pd.read_csv(path, sep='\t', dtype={'image_name':str})

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv

[CPU:  269.9 MB  Avail: 120.06 GB]
return _read(filepath_or_buffer, kwds)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 577, in _read

[CPU:  269.9 MB  Avail: 120.06 GB]
parser = TextFileReader(filepath_or_buffer, **kwds)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__

[CPU:  269.9 MB  Avail: 120.06 GB]
self._engine = self._make_engine(f, self.engine)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine

[CPU:  269.9 MB  Avail: 120.06 GB]
self.handles = get_handle(

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/common.py", line 859, in get_handle

[CPU:  269.9 MB  Avail: 120.06 GB]
handle = open(

[CPU:  269.9 MB  Avail: 120.06 GB]
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed_train.txt'

[CPU:  269.9 MB  Avail: 120.61 GB]
Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 129, in cryosparc_master.cryosparc_compute.run.main
  File "/home/user/CryoSPARC/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py", line 384, in run_topaz_wrapper_train
    utils.run_process(train_command)
  File "/home/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/user/miniconda3/envs/topaz/bin/topaz train --train-images /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/image_list_train.txt --train-targets /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed_train.txt --test-images…)


[CPU:  269.9 MB  Avail: 120.06 GB]
# Training...

[CPU:  269.9 MB  Avail: 120.06 GB]
# source	split	p_observed	num_positive_regions	total_regions

[CPU:  269.9 MB  Avail: 120.06 GB]
Traceback (most recent call last):

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/bin/topaz", line 33, in <module>

[CPU:  269.9 MB  Avail: 120.06 GB]
sys.exit(load_entry_point('topaz-em==0.3.7', 'console_scripts', 'topaz')())

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/main.py", line 148, in main

[CPU:  269.9 MB  Avail: 120.06 GB]
args.func(args)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/commands/train.py", line 140, in main

[CPU:  269.9 MB  Avail: 120.06 GB]
classifier = train_model(classifier, args.train_images, args.train_targets, args.test_images, args.test_targets,

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/training.py", line 607, in train_model

[CPU:  269.9 MB  Avail: 120.06 GB]
num_positive_regions, total_regions, num_images = report_data_stats(train_images_path, train_targets_path, test_images_path, test_targets_path,

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/training.py", line 284, in report_data_stats

[CPU:  269.9 MB  Avail: 120.06 GB]
train_targets = file_utils.read_coordinates(train_targets_path)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/topaz/utils/files.py", line 201, in read_coordinates

[CPU:  269.9 MB  Avail: 120.06 GB]
particles = pd.read_csv(path, sep='\t', dtype={'image_name':str})

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv

[CPU:  269.9 MB  Avail: 120.06 GB]
return _read(filepath_or_buffer, kwds)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 577, in _read

[CPU:  269.9 MB  Avail: 120.06 GB]
parser = TextFileReader(filepath_or_buffer, **kwds)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__

[CPU:  269.9 MB  Avail: 120.06 GB]
self._engine = self._make_engine(f, self.engine)

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine

[CPU:  269.9 MB  Avail: 120.06 GB]
self.handles = get_handle(

[CPU:  269.9 MB  Avail: 120.06 GB]
File "/home/user/miniconda3/envs/topaz/lib/python3.8/site-packages/pandas/io/common.py", line 859, in get_handle

[CPU:  269.9 MB  Avail: 120.06 GB]
handle = open(

[CPU:  269.9 MB  Avail: 120.06 GB]
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed_train.txt'

[CPU:  269.9 MB  Avail: 120.61 GB]
Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 129, in cryosparc_master.cryosparc_compute.run.main
  File "/home/user/CryoSPARC/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py", line 384, in run_topaz_wrapper_train
    utils.run_process(train_command)
  File "/home/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/user/miniconda3/envs/topaz/bin/topaz train --train-images /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/image_list_train.txt --train-targets /mnt/4TSSD/cryosparc_projects/CS-patlab-projects/J85/topaz_particles_processed_train.txt --test-images…)

[ASKrebs]

We're having a similar error. The files are now located in the preprocessed folder. If we copy and rename them from a previously crashed job while a cloned job is running the preprocessing, it can find it.
Then it crashes for us with a cuda error though ...

[CFDavidHou]

I went back to cryoSPARC website for Topaz

https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/topaz

Followed the instruction and solved

In principle, there is a compatibility issue here.

Best,

CFD David