Try a fresh download of Entrez Direct. The current version has an xtract wrapper that launches the appropriate precompiled binary, in this case xtract.Linux.
Xtract was rewritten two years ago, replacing the original Perl implementation, and now always handles recursive data structures. Thus, the capitalized -Pattern is deprecated in favor of the normal -pattern. Furthermore, by default it will only show the top-level data. Additional exploration with -group or -block can go down one level at a time (e.g., -block /Taxon), or do a recursive exploration of each level for deeply-nested data (e.g., -block */Gene-commentary_accession).
