Tee doesn't get whole output from the pipe

I have a script executing commands like:

export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH;./some_app -i $INDEX | tee $LOG
echo "Number of errors: $(grep "ERROR" $LOG | wc -l)"

The problem is probably in the pipe to tee. It does not seem to get the whole output. When the application quits last few lines of the output (usually those containing a fatal error) are missing. When I run the app without pipe to tee I get them in the output.

How can I force script to wait for tee to complete processing of all output?

The fatal error is probably coming out in STDERR (2), not STDOUT (1). You can redirect STDERR into STDOUT with 2>&1 and then the pipe should capture it too.

./some_app -i $INDEX 2>&1 | tee $LOG

If you have buffering issues on top, you could force it into an unbuffered state:

stdbuf -o0 ./some_app -i $INDEX 2>&1 | tee $LOG

As the error messages are normally shown on STDERR (File descriptor 2), you need to redirect both the STDOUT and STDERR to tee:

./some_app -i "$INDEX" |& tee "$LOG"

When you do ./some_app -i $INDEX | tee $LOG you are only redirecting the STDOUT to tee.

|& will cause both the STDOUT and STDERR to be redirected.

If you cant to redirect only the STDOUT (As you were):

./some_app -i "$INDEX" | tee "$LOG"

On the other hand if you want to redirect only the STDERR:

./some_app -i "$INDEX" 2>&1 >/dev/null | tee "$LOG"