ISSUES: 

-auto 

WARNING: Unsupported old command line option '-auto' will be ignored
WARNING: Your old-style command-line options were converted to:  D:\workspace\JABA2\binaries\windows\clustalo\clustalo.exe --outfmt=clustal --log=stat.log --infile=D:\workspace\JABA2\testsrc\testdata\TO1381.fasta --outfile=TO1381.clustal.out -o clustal.aln -v --force
WARNING: This is a beta version of Clustal Omega, for protein only.
For more information try: D:\workspace\JABA2\binaries\windows\clustalo\clustalo.exe --help