I have encountered an issue where in one 2D class selection job, the output file did not contain the particle pick stats, the particle location and ml_properties. When I cloned the job and repeated the selection, the same issue happened again. Then instead of cloning, I created a new 2D class selection job, the output now contained all the information as normal. When I compared the two different 2D class selection jobs, I realized that somehow the input files are different as shown in the below two images. However, both jobs were created in the exact same way and have used the same input file.
I am guessing this problem may be caused by some special circumstances and I am just writing here as reference in case someone encounter the same problem. Please let me know if more information is needed.