Hello, I found two mistakes in the code of the bwa wrapper . The first one comes from the following error message: ----------- File "/galaxy-dist/tools/bwa_wrappers/bwa_wrapper.py", line 79 parser.add_option( '-y', '--ion', dest='ion', action="store_true, help='Ion Torrent data mode using bwasw' ) ^ SyntaxError: EOL while scanning string literal ----------- in the bwa_wrapper.py file line 79: -there is a missing double quote character after sur store_true in the bwasw_wrapper.xml file line 9: -there --ion option must not have a value Till, with those corrections, the mapping with bwa for Ion Torrent does not seem to work properly. My ouput sam file had only the header in it. Best regards Yec'han ================================================ Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _________________________________ Plateforme Genome Transcriptome INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ================================================