Hangs after printing here1

open3.rb

          Open3.popen3(cmd.join(" ")) do |stdin, stdout, stderr, wait_thr|
            input.each_with_index do |record, i|
              if record[:SEQ]
                entry = BioPieces::Seq.new_bp(record)
                entry.seq_name ||= i

                stdin.puts entry.to_fasta
              end

              if output
                output << record
                status[:records_out] += 1
              end
            end
puts "here0"
            stdin.close
puts "here1"
            tree_data = stdout.read.chomp
puts "here2"
            stdout.close
puts "here3"
            exit_status = wait_thr.value
puts "here4"

            raise stderr.read unless exit_status.success?

            if options[:output]
              File.open(options[:output], 'w') do |ios|
                ios.puts tree_data
              end
            else
              puts tree_data
            end
          end