HI all, I looking at the output files of nf-core/mag 5.4.1 The output of checkm2 and busco are missing for the bins from several samples (not always the same)

Hi, have you looked into the .nextflow logs? usually these are a good starting point. There may have been a silent error and it should be logged there 🙂 If it’s inconsistent, my best bet is a memory/job launching issue, it all depends on where and how you launched the pipeline. I have not used MAG before so take my advice with a grain of salt!