Linux – How to copy files from Amazon EC2 server

I am desperately trying to copy some files from AWS EC2 machine but I am struggling with following.

• I am able to copy only some files from already existing folder (although I want to to copy all the files recursively to my local machine)
• scp and rsync complains that path doesn't exist when I create completely new file in some location (let's say /home/ec2-user/a.txt)

The command I am using is

scp -rpi ~/.ssh/my-key.pem  ec2-user@52.29.216.47:/home/ec2-user/a.txt

I created the file under ec2-user with touch a.txt so the permissions should be fine (if that even matters).

Contents of original folder I want to copy is

-rw-r--r--  1 webapp   webapp     90 17. úno  2015 cron.yaml
drw-r--r--  2 ec2-user ec2-user 4096  1. dub 13.09 db-backup
-rw-r--r--  1 webapp   webapp   2703 17. úno  2015 index.php
-rw-r--r--  1 webapp   webapp    189 17. úno  2015 logo_aws_reduced.gif
drwxrwxrwx 15 ec2-user ec2-user 4096  1. dub 17.35 martintour
drw-r--r-- 14 ec2-user ec2-user 4096 30. bře 20.52 master_martintour
-rw-r--r--  1 webapp   webapp    367 17. úno  2015 scheduled.php
-rw-r--r--  1 webapp   webapp   3490 17. úno  2015 styles.css

However only this part is copied

-rw-r--r-- 1 pmensik pmensik   90 úno 17  2015 cron.yaml
-rw-r--r-- 1 pmensik pmensik 2703 úno 17  2015 index.php
-rw-r--r-- 1 pmensik pmensik  189 úno 17  2015 logo_aws_reduced.gif
-rw-r--r-- 1 pmensik pmensik  367 úno 17  2015 scheduled.php
-rw-r--r-- 1 pmensik pmensik 3490 úno 17  2015 styles.css

So it seems like the -r option is not working. And also it doesn't explain why I cannot copy newly created files or folders like I mentioned previously.

The command I used for this is

scp -rpi ~/.ssh/my-key.pem  ec2-user@52.29.216.47:/var/app/current . 

I've already played with changing the permissions but no I am completely lost.