Topaz Extract preprocessing

[leetleyang]

Hi Louis,

That does check out on my end. I did specify the preprocessed folder.

Below are the exact details. Perhaps you could help shed some light on what I’m doing wrong?

Project path /cephfs/ylee/EMP/P19/

Initial Topaz Extract job P19/J12
ResNet16 (64 units)

Second Topaz Extract job P19/J39
Cloned job from P19/J12
Specified /cephfs/ylee/EMP/P19/J12/preprocessed directory

I am deactivating the cryoSPARC conda environment and activating a Topaz-specific one as part of the executable. Would that mess things up?

cryoSPARC v.3.1.0 and Topaz

@jelka @menmt can you try making a bash file that activates your topaz conda environment before invoking topaz? It’ll look something like this: #!/usr/bin/env bash # source ~/anaconda/etc/profile.d/conda.sh conda activate topaz topaz $@ Optionally remove the # from the beginning of the second line if your conda environment is not automatically activated when the shell starts (then specify the correct path to conda.sh if anaconda is not installed at ~/anaconda) Save this in your home director…

Cheers,
Yang