I have just experienced the same trouble. I have traced my failure to a corrupted relations (*.gz) file. In my case this is for a 163 digit composite. At first, the whole upload directory vanished, but it came back after a reboot*. I tried deleting the corrupted file and CADO_NFS wouldn't complete because it was missing. I didn't try removing or editing anything else. Instead, I started msieve to do the Linear Algebra instead of spending more time with CADO-NFS.
*Be careful if you try rebooting! If you are using the default setup for CADO-NFS, the working directory is in /tmp and will be removed during a reboot. You must copy the directory elsewhere to save it.
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