Hi @BShelb
I’m not clear on which score is zero … but I did start up a test run to make sure the tool was working as expected. Maybe this example history will help, too?
See → https://usegalaxy.eu/u/jenj/h/test-mitos
The primary BED output has content (a statistic in the “score” 5th column).
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Tools: both MITOS and MITOS2
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Inputs/parameters: I used all defaults with a super small test file for the first run’s output, then I ran it again and chose to output all of the possible results.
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Results: The “score” field in the BED is the eValue from BLASTN. That value works a bit differently than a BLASTN score value. For eValue, “smaller is better” (more significant**). If the value is too small to write out, then it gets rounded off by BLAST itself. For this case, it flows out to the output from MITOS/2.
- **There is a lot of discussion online about how to interpret a BLAST eValue… too much to write out here. Try a search with “blast evalue 0.0” for more about this.
All of it seems fine to me but let us know if you have questions. 