cryoSPARC Live not seeing data

CryoSPARC Live
1

Hi - I was recently trying to setup a cryoSPARC-Live run on data being acquired by EPU on our G4 Krios. I’m having an odd issue where I can define the folder path the ImageData folder, and normally from here I can set the wild card filter and activate the search recursive and everything is good. However, on this run when I do that cryoSPARC-Live doesn’t see any data. If I go to the main cryoSPARC side however, I can import the same micrographs without any issue. Has anyone seen this before or know where I can even start debugging?

2

Just to confirm:

You mean that you only change the port number in the browser address bar, but the hostname remains unchanged?

3

Correct. That’s all that is changing

4

Please can you try this sequence, escalating to the next step only if the issue hasn’t been resolved at that point:

  1. clear and (re-)start the Live session
  2. add a New exposure group to the session’s configuration and define your data paths and id cards within that new exposure group
  3. cryosparcm restart (which would disrupt running jobs)
  4. reboot the computer
1 Like
5

Wondering if this was resolved? We have the same issue - in V.4.1.2 - I restarted cryoSPARCm - but this is on our cluster - so rebooting the whole system is a nuclear option that will make people unhappy.

6

@DaveBhella Please can you email us the file produced by running
cryosparcm snaplogs?
You may also try to

  1. pause the session
  2. then run
    cryosparcm restart command_rtp
  3. (re-)start the session
7

I have this sitution before. In my case, the time in K3 computer is not correct. As a result, the images wrote to the disk didn’t have correct timestamps (the images have a “future” timestamp). CryoSPARC live seems to ignore these images.
I manage to solve this issue by running a simple command “touch *tif” so that all movies have new timestamps.

8

Thanks all - in the end we updated and restarted CryoSPARC and everything started behaving.

9

@hansenbry @DaveBhella @Pengxin In case you continue to “not see” newly arriving data in CryoSPARC Live:
We released patch 230329 for CryoSPARC v4.2.1 as a fix for CryoSPARC Live not importing new files.
You can find patch instructions here.

CryoSPARC needs to be restarted after applying this patch.

10

Hello,

We updated with the patch (cryoSPARC restarted and even the system rebooted), but still cryoSPARC live doesn’t see any exposures while cryoSPARC can see them fine.

Thanks,

11

Hi @rosel Please can you email the tgz file created by the command
cryosparcm snaplogs

12

@rosel I’m seeing the following error in your logs:

OSError: [Errno 40] Too many levels of symbolic links: '/cem1data1/cryosparcdata1/facility/APO_20230205/rawdata/FoilHole_4327094_Data_4321776_4321778_20230207_144550_Fractions.mrc'

This looks like a symbolic link that may be pointing to itself. Could you check the files in the /cem1data1/cryosparcdata1/facility/APO_20230205/rawdata/ to see if there is anything inconsistent?

13

@hansenbry @DaveBhella @Pengxin if you installed the latest patch, please let me know if you’ve seen this issue come up again

14

Hi,

I don’t see this issue after installing the latesr patch.

-Pengxin

1 Like
15

Hello,

The symbolic link for the files listed are broken since the data on the server was removed. But we are having the same problem with newer data with the correct symbolic link or data saved in the local disk. The new log file was sent.

Our problem is not seeing new data, but cryoSPARC live doesn’t see any exposures, mrc or tiff. By the way, our data was collected using EPU. Not sure if it is related to our problem.

Thank you,

16

Are both the mrc and tiff files multiframe movies, as opposed to motion-corrected micrographs?

17

Yes. They are multiframe movies. The live was working under cryoSPARC v4.0.1 and then cryoSPARC was updated to v4.2.1 because the v4.0.1 issue of not importing any EPU generated tiff files.

18

@rosel Please could you email us:

  1. the “session document” for the Live session where which can be obtained (please substitute correct project and session UIDs) via
    cryosparcm rtpcli "get_session_doc('P23', 'S4')" > P23_S4_doc.txt
  2. the output of cryosparcm snaplogs (again)
19

Hi, I’m getting a similar error in September 2023.

CryoSPARC live is apparently unable to find exposures. I’m running the reference-based motion correction beta version (v4.4). I have used cryoSPARC live a few times in the past with no such issues, but now I cannot get any new datasets to import. If I explicitly specify the data directory in normal cryoSPARC I can import and process the data, so it seems to only be a cryoSPARC live issue.

I’ve tried:

  1. Stopping and restarting cryosparc
  2. Running touch on some of the data files.
  3. Deleting the project/session and recreating it

Two potentially relevant complications are that:

  1. My datasets live on a ‘FSX for Lustre’ file system
  2. I instantiated the cryosparc live session using the RTP cli following the instructions here. This worked successfully to initiate cryosparc live sessions for two datasets yesterday, and the resulting session looks exactly like I’d expect if I had started through the webUI. However, it’s obviously not working now, and this was the main thing I changed since things stopped working.
  3. I have since tried creating a project and the live session entirely through the webUI and exposures are still not found.

Happy to send any logs that would be helpful for debugging. Let me know what I should do!

Eugene

20

Okay, weird, quick update on this. I noticed I had another cryosparc live session running (but not doing anything, it had processed an entire dataset but had not been ‘paused’). When I stopped it, the one that hadn’t been working started right up and found all of its exposures.

I’d still like to investigate this and debug, because something is happening that I don’t understand and I would like to be able to smoothly instantiate multiple cryoSPARC live sessions in the future/