I'm reading a file line by line and running ssh or ffmpeg, only the first line gets processed!

When reading a file line by line, if a command inside the loop also reads stdin, it can exhaust the input file. For example: 

   1 # Non-working example
   2 while IFS= read -r file; do
   3   ffmpeg -i "$file" -c:v libx264 -c:a aac "${file%.avi}".mkv
   4 done < <(find . -name '*.avi')


   1 # Non-working example
   2 while read host; do
   3   ssh "$host" some command
   4 done < hostslist

What's happening here? Let's take the first example. read reads a line from standard input (FD 0), puts it in the file parameter, and then ffmpeg is executed. Like any program you execute from BASH, ffmpeg inherits standard input. However, ffmpeg additionally uses standard input to detect quit commands indicated by user input of q, thus sucking up all the input from the find command and starving the loop.

Use the -nostdin global option in ffmpeg to disable interaction on standard input: 

   1 while IFS= read -r file; do
   2   ffmpeg -nostdin -i "$file" -c:v libx264 -c:a aac "${file%.avi}".mkv
   3 done < <(find . -name '*.avi')

Alternatively you could use redirection at the end of the ffmpeg line: </dev/null. The ssh example can be fixed the same way, or with the -n switch (at least with OpenSSH).

Sometimes with large loops it might be difficult to work out what's reading from stdin, or a program might change its behaviour when you add </dev/null to it. In this case you can make read use a different FileDescriptor that a random program is less likely to read from: 

   1 while IFS= read -r line <&3; do
   2   ...
   3 done 3< file

In bash, the read builtin can also be told to read directly from an fd (-u fd) without redirection, and since bash 4.1, an available fd can be assigned ({var}<file) instead of hard coding a file descriptor. 

   1 # bash 4.1+
   2 while IFS= read -r -u "$fd" line; do
   3   ...
   4 done {fd}< file
   5 exec {fd}<&-