Tools should not write empty fail files

[Jason Vander Heiden]

Remove opening of empty fail files. See changeo issues:

• https://bitbucket.org/kleinstein/changeo/issues/103/tools-should-not-create-empty-fail-file
• https://bitbucket.org/kleinstein/changeo/issues/119/convert-output-handle-checks-to-try-blocks

[Jason Vander Heiden]

Done in d069248.