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Run jobs

Setup your first job

To setup your first job, click on the respective colum in the 2D grid: if you want to process movies, you will likely want to start a MotionCor job which you can find in the Pre-processing column. For uploaded particles, you can start a Class2D job in the Class2D column. Add a job of the desired type by hovering over the grid and clicking the "+". you will be prompted to select a JobType and can select one of your linked datasets as input source. Confirm your selection by clicking Setup job, and the job will then be displayed as a tile.

Job view

Clicking on the tile will present you the job view. The Job view is divided into 3 main tabs: Setup, Monitoring and Results which are displayed at the top and, once active, can be toggled through by the arrows on the top.

Specify parameters

Specify the parameters within the Setup tab. Once you specified all parameters, click Save to save your job draft. If you missed a required parameter, a warning will be displayed at the bottom and highlight which input is still required. Careful: If you get a warning, the job is not saved yet!

After saving, you can change parameters by simply adjusting them and clicking Update at the bottom.

Run your first job

Once you confirmed your parameters by hitting save, you can start the job by hitting Run Job at the bottom right. This will scroll the page up and update the status of the Monitoring page. Once the job starts, the Job view will automatically switch to the monitoring tab.

Monitoring jobs

The monitoring tab will display the log of the running job. You can always leave this job and come back later to check on your job. The respective jobtile in the project overview will indicate the status of the job. E.g. if the job is still running, the job status light will pulse.

Inspecting results

After a job is finished, the job will automatically switch to the results tab. You can inspect the files in the fileviewer and download them by clicking the arrow next to the file when hovering over it. In particular the logfile.pdf can be useful to check some of your results. For the Autopicking job, you can inspect the picked coordinates on the respective micrograph. Downloading 3D maps after refinement or classification jobs to your local laptop will be useful to inspect the results using, e.g., Chimera.

Run subsequent jobs

Similar to your first job, hover over the job grid in the project overview and click on "+" to add a new job. Instead of using a dataset, select a previous job as input source. The new job will then be displayed under its parent job, and subsequent jobs will be connected by arrows.