命令行写错了，你这个：01.prepare_data.sh: line 47: /share/work/my_demo/biosoft/TransDecoder/latest/util/gff3_file_to_proteins/biosoft/TransDecoder/latest/util/gff3_file_to_proteins.pl: No such file or directory

文件路径写错了，：/share/work/my_demo/biosoft/TransDecoder/latest/util/gff3_file_to_proteins/biosoft/TransDecoder/latest/util/gff3_file_to_proteins.pl