Weird data loading error

Troubleshooting
1

Hi,

I installed CryoSPARC on a GPU machine quite a while ago and have used it for a number of tries including the test TRVP1 data set without issues. Recently, the GPU machine was relocated to another place behind a firewall. I ran into issues when I tried to run CryoSPARC remotely from a Windows computer. One issue is that I cannot load the TRPV1 test data as I did before (error of which is copied below). Originally I thought it is an issue with remote access only. After I double check on the computer locally. I got the same error. Can someone take a look and give some clue? By the way, I found it works fine with particle files that generated locally e.g. particle.star generated by Extract in Relion.

Launched job 2n8m52vddkphwQK3x
License is valid.
Job Type: visualize_dataset Job ID: 2n8m52vddkphwQK3x
Assigned Slots: RAM: None GPU: None
Visualizing Dataset ID qv22d7YmoqLbGhwKC
Loading Dataset …
---- Loading File Set. Type: star Path: /mnt/data1/software/cryosparc/run/bulk/./local_fs/home/user/TRPV1/empiar10005_trpv1.star
Traceback (most recent call last):
File “/mnt/data1/software/cryosparc/cryosparc-compute/sparcjob.py”, line 118, in
dataset = dataio.dataset_factory(current_dataset_params, do_cache=False, do_datasign_estimation=False)
File “/mnt/data1/software/cryosparc/cryosparc-compute/dataio/init.py”, line 18, in dataset_factory
do_cache=do_cache)
File “/mnt/data1/software/cryosparc/cryosparc-compute/dataio/load.py”, line 63, in filesets_into_dataset
images = extension_map[meta_type](dataset, meta_input)
File “/mnt/data1/software/cryosparc/cryosparc-compute/dataio/load.py”, line 307, in star_into_dataset
assert (‘rlnDetectorPixelSize’ in labels and ‘rlnMagnification’ in labels) or ‘psize’ in dataset.mscope_params, “The input star file does not contain rlnDetectorPixelSize and rlnMagnification, and a pixel size (psize) was not set in dataset creation.”
AssertionError: The input star file does not contain rlnDetectorPixelSize and rlnMagnification, and a pixel size (psize) was not set in dataset creation.

Thanks,

Guobin Hu

2

Hi Guobin

I’m not a cryosparc expert but the error quoted above seems to want the rlnDetector pixelsize and mag .Magnification is a place-holder value in relion2 but pixel size is definitely needed.Is something weird with your star file?

3

Hi Joshua,

Thanks for your attention and reply! What you pointed out does make sense to me. On the other hand, the input file is actually the TRPV1 test data I downloaded and which I tested before. Fortunately, I tested a few the files that were generated locally and the program works.

Best,

Guobin

4

Just an update for the issue. I was able to load the data when I input both meta data file and image data file at the same time.

5