Don't run the same OS, but have had the same issues and sharing what was discovered. The error isn't accurate per say ... but related.
The backup routine creates a hash named directory in moodledata/temp/backup/ that it uses for building the various pieces to a course backup. Directory name looks something like 23asoqwerudp4235.
A large course will take time so one could watch the process to see if it indeed did complete but could NOT 'cp' the backup to it's desitnation ... which is what my issue was (use of cp rather than mv).
So check out your moodledata/temp/backup/ directory for those long hash named directories.
If you have one there, change into it and see if there is not already residing there a large .mbz file. If there is, one can 'mv' to some other location:
mv backup-moodle2-course-6-ma101-20150129-1623.mbz /home/backup/
It is safe to remove manually those hash named directories on failed backups.
Try your command line backup like so: php backup.php --courseid=6 --destination=./
Then ls *.mbz if it completes. One could then mv *.mbz /whereever/
Another item to check/verify, max_input_vars setting of your DB server. MySQL has a default lower than the number needed to do large backups.
Granted this is not a solution, but something to investigate/try ... you said you needed those backups! ;)
'spirit of sharing', Ken