Currently (as of version 0.22), Gnuastro cannot write unsigned 64-bit integer types in a FITS table column. The problem can be reproduced with the example code in the P.S.

During a recent discussion on the fitsbits mailing list, the following solution was suggested: "I have come across TZEROn = 9223372036854775808 to represent unsigned 64-bit integers (SDSS DR15 I think)."

We can implement this within Gnuastro's FITS library table reading/writing features to store unsigned 64-bit integers.

P.S. Reproducing the problem:

$ cat table.txt
# Column 1: ID [counter, u64] ID of object
123

$ asttable table.txt -o table.fits
asttable: gal_fits_type_to_bin_tform: type uint64 not recognized for FITS binary table TFORM