non-standard characters in input files/folders

[noncodo]

Using node-local storage speeds up IO heavy tasks significantly on SGE/PBS systems. The Trinity mods make use of this, however as a list of commands is intrinsically being generated by the Trinity code, it writes the TMP (node-local) path for the files. We patched this by using SED to replace the tmp with output directories, however SED will not work if special characters are in the path. In my example, the filenames had multiple '.' characters, which ultimately caused a bug (the trinity_butterfly couldn't find the TMP files).

Recommendation: specify that the filenames and paths contain no special characters.