Project P3 Job J66 Startedīeginning Topaz denoising command by running command /programs/x/topaz/0.2.3/bin.capsules/topaz denoise -device -1 -format mrc -normalize -patch-size 1536 -patch-padding 256 -output /data2/P4/J66/denoised_micrographs -lowpass 1 -gaussian 0 -inv-gaussian 0 -deconv-patch 1 -pixel-cutoff 0 -deconvolve -model unet Checking outputs for output group denoised_micrographs
Intersection of output and passthrough has 237 items Passing through outputs for output group denoised_micrographs from input group micrographs Converting Topaz outputs to cryoSPARC outputs. Topaz denoising command complete in 14.529s. RuntimeError: CUDA error: invalid argument cov = F.conv2d(x.unsqueeze(0).unsqueeze(1), x_c.unsqueeze(0).unsqueeze(1)).squeeze() File "/programs/x86_64-linux/topaz/0.2.3/lib/python3.7/site-packages/topaz/denoise.py", line 147, in spatial_covariance cov = spatial_covariance(x, n=width, s=s) File "/programs/x86_64-linux/topaz/0.2.3/lib/python3.7/site-packages/topaz/denoise.py", line 194, in estimate_unblur_filter f,cov = estimate_unblur_filter(x, width=width, s=s) File "/programs/x86_64-linux/topaz/0.2.3/lib/python3.7/site-packages/topaz/denoise.py", line 304, in correct_spatial_covariance x = dn.correct_spatial_covariance(x, patch=deconv_patch) File "/programs/x86_64-linux/topaz/0.2.3/lib/python3.7/site-packages/topaz/commands/denoise.py", line 285, in denoise_image File "/programs/x86_64-linux/topaz/0.2.3/lib/python3.7/site-packages/topaz/commands/denoise.py", line 531, in main Using Topaz provided pretrained model.īeginning Topaz denoising command by running command /programs/x/topaz/0.2.3/bin.capsules/topaz denoise -device 0 -format mrc -normalize -patch-size 1536 -patch-padding 256 -output /data2/P4/J48/denoised_micrographs -lowpass 1 -gaussian 0 -inv-gaussian 0 -deconv-patch 1 -pixel-cutoff 0 -deconvolve -model unet Starting Topaz process using version 0.2.3.
TOPAZ DEJPEG LATEST LICENSE
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. and cryoSPARC do not license Topaz nor distribute Topaz binaries. Topaz-Denoise: general deep denoising models for cryoEM. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Topaz is a particle detection tool created by Tristan Bepler and Alex J. Importing job module for job type topaz_denoise. Master running v2.15.0, worker running v2.15.0
Running job on master node hostname mamba Launching job on lane default target mamba. This is the denoise log (there is some cude error) topaz picking work OK: License is valid. Job is finish as completed but there is not images when it finish and the output can’t be used in any down stream job. Topaz denoise 0.2.3 don’t work in v2.15.0.
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