Add check for existing Project_ directories

		return;

	}

	# Check to see if we have any Project directories

	my $basecalls_path = "$RUNFOLDER/Data/Intensities/BaseCalls";

	my $basecalls_handle;

	opendir($basecalls_handle, $basecalls_path) or do {

		log_msg(<<"EOF");

The BaseCalls directory does not exist, is not a directory, or cannot be read.

Please make sure you are running this command with a valid run folder!

The directory we are trying to open is: $basecalls_path

The error we are getting is: $!

EOF

		return;

	};

	while (readdir($basecalls_handle)) {

		# Find any directories whose name starts with "Project_"

		next unless $_ =~ m{\A        # Start of string

		                    (         # Start capturing match

		                    Project_  # "Project_"

		                    [a-z0-9]+ # One or more letters/numbers

		                    )         # End capture

		                    \z        # End of string

		                   }xims;

		# Rename the directory (this might recurse)

		log_msg(<<"EOF");

We found an existing Project directory: $1.

We are renaming this to $1.old.

(If that directory already exists, we'll add another ".old" to that one,

and so on, and so on, and ....

EOF

		my $old_project_path = "$basecalls_path/$1";

		directory_rename($old_project_path);

	}

	# Get ready to run the analysis command

	log_msg("Running the analysis!\n");

	log_msg("Analysis command: " . join(' ', @RUNCOMMAND) . "\n");

		$analysis_buffer = '';

	}

	waitpid($analysis_pid, 0);

	close($output_handle);

	# Clean up from the analysis command

	my $analysis_exit_code = $? >> 8;

		return undef;

	}

}

# Append .old to a directory

sub directory_rename {

	my ($path) = @_;

	my $new_name = "$path.old";

	if (-r $new_name) {

		directory_rename($new_name);

	}

	rename($path, $new_name);

}