We have installed and are using Cryosparc 3.1 version through ssh (HPC). I am able to run most of the jobs normally. I have two datasets, collected on the same day and I’ve been processing them in separate folders. From one of the datasets, I have gotten desirable ‘sideview’ classes which I am now trying to use as a template for particle picking in the other data set. To do that, I need to export that job and import it in my other dataset working folder. When exporting via cryosparc, no problems are reported, however, when i navigate to the folder of the other dataset, and try to import the job, I get the following error:
Unable to import job from ///P17/J435/ into P17: string index out of range
I made sure the job export is complete and I gave the absolute path that leads to the job.json file (didn’t include the filename in the path).
This ///P17/J435/ and not this ///P17/J435/job.json
You can run this command from the shell on your master node. If you’re physically near the master node, you can open up a terminal and run this command. If you’re not, you will have to ssh into the master node first.
I am connected via ssh to the master node so I can search for the file. Could you share a command string to do that? I am fairly new to linux and would help me if you can.
Great, the command is cryosparcm log command_core. When you run this command, it will output all the logs from the server into your shell. You can then copy and paste the contents here.
During the installation process, did you select ‘no’ for the option to add cryoSPARC to your PATH variable? If so, to call cryosparcm first enter the cryosparc_master directory, then run:
We use HPC that is being maintained and all the software is installed as a service to our labs. We end up having no control of how modules and programs are installed. I am not sure why and how but this is what I get when I execute the commands you just sent.
[nxb318@cgput001 ~]$ cryosparc_master
bash: cryosparc_master: command not found
[nxb318@cgput001 ~]$ ./bin/cryosparcm log command_core
bash: ./bin/cryosparcm: No such file or directory
Do you happen to know where cryosparc is installed?
If you do, the first thing would be to navigate to the cryosparc2_master folder.
To do so, type: cd cryosparc2_master
Then you can run the command ./bin/cryosparcm log command_core
You can follow this tutorial for a great guide to the linux command line:
Thank you very much for the CLI guide. I know where CS is installed, however, I do not have permission to view or edit the contents of that folder since the PC is in the HPC. This all complicates the matters, so if I don’t find a workaround, I will msg you in this thread.