Cannot use topaz on V4.1.1

Install, Configure and Update
1

Hello,
I am new to CryoSPARC. I am trying to use topaz for particle picking.

I have installed topaz 0.2.5a and works fine from command line.

I am trying to build a job ‘Topaz Extract’ and gave location of topaz on “Path to Topaz executable”.
I am constantly getting error saying ######. AssertionError: Cannot determine topaz version, command “/raid-18/LS/smarius/karkip/topaz.sh --version” did not produce valid output: “/raid-18/LS/smarius/karkip/topaz.sh: line 19: exec: topaz: not found”

what is missing here? Any help will be appreciated.

Thank you!

2

Welcome to the forum @prabin .
Please can you post the output of the command

cat /raid-18/LS/smarius/karkip/topaz.sh
3

Hi @wtempel. Thank you for the response. Here is the content of topaz.sh

#!/usr/bin/env bash

if command -v conda > /dev/null 2>&1; then

conda deactivate > /dev/null 2>&1 || true # ignore any errors

conda deactivate > /dev/null 2>&1 || true # ignore any errors

fi

unset _CE_CONDA

unset CONDA_DEFAULT_ENV

unset CONDA_EXE

unset CONDA_PREFIX

unset CONDA_PROMPT_MODIFIER

unset CONDA_PYTHON_EXE

unset CONDA_SHLVL

unset PYTHONPATH

unset LD_PRELOAD

unset LD_LIBRARY_PATH

source /raid-18/LS/smarius/karkip/anaconda3/etc/profile.d/conda.sh

conda activate topaz

exec topaz $@

4

Thanks @prabin The script looks plausible to me

When you run topaz on the command line, do you specify the absolute path of the topaz executable?
What are the outputs of the commands

which topaz
conda activate topaz
which topaz
conda list topaz
conda deactivate
5

Hello @wtempel ,
thank you for the response. To run topaz from command line I used script from topaz github account. one of the script looks like this:

#!/bin/bash
source activate topaz

mkdir -p data/EMPIAR-10025/processed
mkdir -p data/EMPIAR-10025/processed/micrographs

topaz preprocess -v -s 8 -o data/EMPIAR-10025/processed/micrographs/ data/EMPIAR-10025/rawdata/micrographs/*.mrc

topaz convert -s 8 -o data/EMPIAR-10025/processed/particles.txt data/EMPIAR-10025/rawdata/particles.txt

Note: topaz/tutorial/01_quick_start_guide.ipynb at master · tbepler/topaz · GitHub. this tutorial run with out any error on my command line.

Screenshot 2024-08-21 at 1.10.28 PM
Screenshot 2024-08-21 at 1.10.28 PM1490×500 163 KB

6

The outputs of the which topaz commands suggest to me that there is an entire stack of conda environments active, and I do not know in which way they are loaded on your computer.
You could try running a Topaz job within CryoSPARC after either:

  1. replacing the last line of the /raid-18/LS/smarius/karkip/topaz.sh with the line
    exec /raid-18/LS/smarius/karkip/anaconda3/envs/topaz/bin/topaz $@
  2. or specifying
    /raid-18/LS/smarius/karkip/anaconda3/envs/topaz/bin/topaz

for the Topaz job’s Path to Topaz executable parameter.