Sometimes input errors are caused because of non-sorted inputs. Try using these:
Picard SortSam: Sort SAM/BAM by coordinate or queryname.
Samtools Sort: Alternate for SAM/BAM, best when used for coordinate sorting only.
SortBED order the intervals: Best choice for BED/Interval.
Sort data in ascending or descending order: Alternate choice for Tabular/BED/Interval/GTF.
VCFsort: Best choice for VFC.
Tool Form Options for Sorting: Some tools have an option to sort inputs during job execution. Whenever possible, sort inputs before using tools, especially if jobs fail for not having enough memory resources.