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rsync -rave "ssh -i ~/Desktop/mypemfile.pem" /users/myusername/dev/myproject/wp-content/uploads/* ubuntu@myinstance(changed name).compute.amazonaws.com:/var/www/html/production/wp-content/uploads --omit-dir-times

/var/www/html/production/wp-content/uploads/2018/02 has 50 extra files that are not present in /users/myusername/dev/myproject/wp-content/uploads/2018/02

Why aren't they copied over to /Users/.... ?

rsync outputs this:

building file list ... done

sent 678984 bytes  received 20 bytes  452669.33 bytes/sec
total size is 3691754591  speedup is 5437.01

but does nothing.

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    looks to me like you're syncing from /users/... to /var/www, without the --delete flag, which means it's OK that the destination has more files. Is that the intention with your command? – Jeff Schaller Feb 14 '18 at 21:09
  • I would like to make sure all files existing in my EC2 instance below ../wp-content/uploads/*.* (recursively) find . their way into my local machine /users/....... /wp-content/uploads - I know I can scp, but scp doesn't do incremental..... I need an incremental copy really. – JasonGenX Feb 14 '18 at 21:17
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    You have the arguments backwards. It's rsync source destination – Barmar Feb 14 '18 at 22:19
  • You mention /Users/ in your text but your command uses /users/. UNIX/LInux-based systems are case sensitive and this difference might be important. – roaima Feb 14 '18 at 23:31
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The rsync command uses the same structure as cp and mv: the source leads the destination on the command line:

rsync  --flags...  /source/path  /destination/path

So in your instance the reason nothing is being copied to /users/ (note, not /Users/ as in your question text) is because you are copying from /users to the remote AWS target.

If you wanted to copy from AWS to your local filesystem you should be using a command like this (split over three lines; note that the trailing \ indicates a continuation to the next line):

rsync -avO -e "ssh -i ~/Desktop/mypemfile.pem" \
    ubuntu@myinstance(changed name).compute.amazonaws.com:/var/www/html/production/wp-content/uploads/ \
    /users/myusername/dev/myproject/wp-content/uploads/

Some optimisations: don't use * on the source list (just ensure the path ends with /), and -r is implied by -a.

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