Hi @MPG
Check these two items. The first may or may not be OK (worth checking), and the second is likely a content problem (mismatched chromosome names). Both might need to be adjusted.
Make sure that the pairs are entered in the same order on the tool form, and that none of the ends of any pairs are omitted. You can click into the “i” Job Details page to see what was originally submitted to check (even for failed jobs). If you have many paired end datasets, using dataset collections would help: Search Tutorials
The reference genome was sourced from UCSC when we indexed it on the server.
All other inputs must use that same genome/build, including the same chromosome naming formats, or tools will either ignore the mismatched input or trigger a failure.
The reference annotation (gene model) was sourced directly by you… from Ensembl (?). They use a different chromosome name format than UCSC. Where to get the annotation with UCSC chromosome names is in this prior Q&A:
Nothing else pops out. So, please try using the UCSC GTF instead with rerun(s). If any still fail, please send in a bug report from one of the red error datasets, and include a link to this topic in the comments so we can link the two for context. Also, please leave all datasets undeleted (inputs + outputs, successful or failure) for review.
Thanks!