Blank qc_outcome column

[bajwamoneeb]

I used Phoenix on Terra and I got some samples as having a blank for qc_outcome and I am not sure what that signifies or why that is; is it passing or failing? They look to be good quality based on other metrics and pipelines we ran them thru.

[jvhagey]

So it looks like both samples had a failure during the second to last step MultiQC that is specific to that program.

When I back track a bit it looks like something odd is happening with the kraken file:

To debug this further I will need to run the samples on my side to get the intermediate files as Terra doesn't copy them if there is a failure. I will send you an email to set up a sharefile folder.