If you have a look at /usr/bin/filebeat you will see it sets all the correct paths:
#!/usr/bin/env bash
# Script to run filebeat in foreground with the same path settings that
# the init script / systemd unit file would do.
exec /usr/share/filebeat/bin/filebeat \
-path.home /usr/share/filebeat \
-path.config /etc/filebeat \
-path.data /var/lib/filebeat \
-path.logs /var/log/filebeat \
"$@"
So in case you want to call the binary directly, you also have to set paths manually as otherwise it falls back to the default paths which are relative to your current directory.
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