Topaz Train: preprocess: error

Hi all,

I am trying to run Topaz in cryoSparc but got this error message. Does anyone know how to fix that? Thanks.

License is valid.

Launching job on lane default target dubochet ...

Running job on master node hostname dubochet

[CPU: 86.1 MB]   Project P5 Job J36 Started

[CPU: 86.1 MB]   Master running v2.14.2, worker running v2.14.2

[CPU: 86.4 MB]   Running on lane default

[CPU: 86.4 MB]   Resources allocated: 

[CPU: 86.4 MB]     Worker:  dubochet

[CPU: 86.4 MB]     CPU   :  [8, 9, 10, 11]

[CPU: 86.4 MB]     GPU   :  [1]

[CPU: 86.4 MB]     RAM   :  [2]

[CPU: 86.4 MB]     SSD   :  False

[CPU: 86.4 MB]   --------------------------------------------------------------

[CPU: 86.4 MB]   Importing job module for job type topaz_train...

[CPU: 161.2 MB]  Job ready to run

[CPU: 161.2 MB]  ***************************************************************

[CPU: 161.2 MB]  Topaz is a particle detection tool created by Tristan Bepler and Alex J. Noble.
- 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 (209) doi:

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:

[CPU: 161.5 MB]  Starting Topaz process using version 0.2.3...

[CPU: 161.5 MB]  Random seed used is 853275478

[CPU: 161.5 MB]  --------------------------------------------------------------

[CPU: 161.5 MB]  Starting preprocessing...

[CPU: 161.5 MB]  Starting micrograph preprocessing by running command /home/cryosparc_user/anaconda3/bin/topaz preprocess --scale 4 --niters 10 --num-workers 4 -o /home/cryosparc_user/Documents/Dylan/Tutorial/P5/J36/preprocessed [MICROGRAPH PATHS EXCLUDED FOR LEGIBILITY]

[CPU: 161.5 MB]  Preprocessing over 4 processes...

[CPU: 161.7 MB]  usage: topaz preprocess [-h] [-s SCALE] [--affine] [--sample SAMPLE]

[CPU: 161.7 MB]                          [--niters NITERS] [-a ALPHA] [-b BETA] [--metadata]

[CPU: 161.7 MB]                          [-d DEVICE] [-t NUM_WORKERS] [-o DESTDIR]

[CPU: 161.7 MB]                          [--format FORMAT_] [-v]

[CPU: 161.7 MB]                          files [files ...]

[CPU: 161.7 MB]  topaz preprocess: error: the following arguments are required: files

Here is the job’s log file:

================= CRYOSPARCW =======  2020-02-27 19:03:33.483306  =========
Project P5 Job J36
Master dubochet Port 39002
========= monitor process now starting main process
========= monitor process now waiting for main process
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat

Hi @mizz_em,

Could you try installing Topaz into an environment with Python 2.7 and then running that executable?

I was also able to reproduce the error by tricking the job into thinking the micrographs dataset input had 0 micrographs. This indicates that there is an issue with the micrographs input into the Topaz Train job. Could you look through the micrograph processing again to check for possible issues?

Jay Yoo