using ms_convert.exe and converting a file named PG01-0-1_216994_01_0_1_1_01_10000001.wiff but the name of the mzML file is PG01-0-1_216994_01_0_1_1_01_10000001-216994_1_1_01_10000001.mzML so the name of the input is not the same as the name of the output file.
converting thermo or agilent files works fine the name remains the same for this kind of raw-data.