The input for FreeBayes is a mapped BAM dataset. The input to the mapping tool in used upstream (Bowtie2, BWA/MEM) would contain quality scores, even if provided as default values (using a tool like Combine FASTA and QUAL into FASTQ). Perhaps the jobs were not run with a mapped BAM input?
At Galaxy Main https://usegalaxy.org, I see at least one successful FreeBayes job in your recent histories. It uses proper inputs and produces the correct output. I wasn't able to find the jobs with this type of input/output.
If you still need help, and are working at Galaxy main, an email can be sent to firstname.lastname@example.org from your registered account. Include details about the exact history (share link to history) and FreeBayes output dataset numbers that represent this issue. Make sure all inputs/outputs are left undeleted for full review/feedback. Undelete (if just deleted) or reproduce (if permanently deleted). If there is a problem, we'd like to clarify and fix it.
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