Hi all,
I ma processing negative stain micrographs and trying to use topaz train to better pick my particles that are hard to find. I get the following error.
Kindly help. Thank you.
Hello!
Iâm new from cryoSPARC and here the students will use Topaz too.
According to this guide (https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc/deep-picking/deep-picking) the latest version of Topaz compatible with cryoSPARC is 0.2.3 in your image I see that you are using version 0.2.4 and maybe this could be the problem.
This guide does not have a publication date so I believe it is the last valid instruction for installing Topaz.
Try to downgrade topaz version.
Regards.
Hi chari1,
This error is coming from Cryosparcâs Topaz wrapper script. It looks like you put the scale value in correctly as 16. This script multiplies by the pixelsize. Can you check on that?
Best,
-Alex
Hi Alex,
I tried 2 different downsampling factors - 4 and 16. I get the same error.
Hi chari1,
Can you check the pixelsize of the images?
Thanks,
-Alex
I have the same error with a/pix of 2.18
command: /programs/x/topaz/0.2.4/bin/topaz preprocess --scale 4 --niters 200 --num-workers 20 -o
Dose anyone figure the problem?
Topaz and CS both run under Python3 and I try Topaz 0.2.3/4/5 all with the same error.
The A/pix is 2.18
CPU: 218.1 MB] Traceback (most recent call last):
File âcryosparc_worker/cryosparc_compute/run.pyâ, line 84, in cryosparc_compute.run.main
File â/data2/software/cryosparc/cryosparc2_worker/cryosparc_compute/jobs/topaz/run_topaz.pyâ, line 224, in run_topaz_wrapper_train
new_psize = psize_A_list[idx] * downsampling_scale
TypeError: canât multiply sequence by non-int of type ânumpy.float32â
Hi all, this is indeed a bug in cryoSPARC. Weâll be issuing a fix in an upcoming release. Will update here when thatâs available.
A fix for this is included in v3.2, released March 29, 2021. Release notes available here: https://cryosparc.com/updates
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