Do all annotation files, the meta data files and the lexicon have consistent line terminators? DOS requires a combination of CR (Hex 0D) followed by LF (Hex 0A), while UNIX requires only the LF (Hex 0A). Mixed usage of the line terminators may be caused by working on mixed platforms. They may cause problems when parsing the annotation files later.
A simple test for all lines in a annotation file to be DOS-compatible would be5.2:
... cat $file | tr '\r' '&' | grep -v '&$' > /dev/null if ( $status == 0 ) then echo "WARNING: $file contains lines not DOS-compatible" endif ...To check for UNIX conformity, simply delete the grep option -v5.3.