Kevin M. Kocot

I am having the same issue when trying to use --crf here. I'm using braker.pl version 2.1.6 and Augustus 3.4.0.

Hi all. Switching back from Augustus 3.4.0 to 3.3.3 fixed this issue for me for what it's worth.

Hello, I have been having the same "bwa failed, skipping sublib" issue. It persists if I try spades with the --continue option. I trimmed these data with Trimmomatic and here...

Thanks for referencing this issue - I previously assumed that was my problem but my .fastq PE headers now match and I'm still getting the same error.

Thanks @asl. That is almost certainly my problem. I'll try again without --careful.

Just to follow up - my assemblies completed normally when I removed the --careful flag.

Providing any non-empty files from the errors directory might be helpful to the admins.