The "Fstat.out" file is the file that keeps track of intermediate results, the "Fstat.out.ckp" ist the checkpoint file that keeps some metainformation, including the expected lenght of the Fstat file "Fstat.out".
When the App is (re-)started, it first reads the checkpoint file (if present), then tries to read in the Fstat file with the information it got. If that works, the data is read into an internal structure that is called the "toplist", as you can see in the second block of stderr output. If the Fstat file doesn't agree with the information in the checkpoint file, it is considered to be corrupt, and calculation starts from the beginning.
I suspect that somehow a checkpoint file was left in the slots directory from a previous run, as this situation happened right at the beginning of the calculation. The Fstat file indeed is empty at the beginning of the calculation, which is not an error.
To save time in FileIO, new (intermediate) results get only appended to the Fstat file instead of rewriting the whole file every time. To not clobber the harddisk, however, when this grows too large, it is "compactified", i.e. newly written as a whole.
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