trinity from HISAT2 unaligned reads

Hi @Pedro

This just means the job queued. That is normal and expected. See → Understanding job statuses

This is just a top level error shown inside the dataset. The rest of the job logs will likely have more informative messages, and the kinds of input/parameter details others will need to help you more. This is how and where to find them → Troubleshooting errors

That said, if the reads didn’t map to a reference genome that is a strong clue that the data is not from that species. It could be contamination or even low quality data of some type. Meaning, those reads may not assemble for the same reasons that they didn’t map.

Maybe try to find out what those reads are? The QA steps might have revealed something, so start with the FastQC reports.

Other ideas



Give those a review first. I’m not clear on why you were assembling to start with, so please explain that part if you need more help.