Hey, I am currently running MAG, and I see that it...
# meta-omicst
Thomas Haverkamp
10/30/2025, 10:29 AMHey, I am currently running MAG, and I see that it is doing the assemblies for both megahit and spades. After that it runs the mapping, and I set it to binning_map_mode": "own".
I am now wondering why the binning for the finished samples after mapping is not starting in my run? Is that deliberate behaviour, that it first needs to finish all the mapping?
j
James Fellows Yates
11/03/2025, 9:03 AMA technical reason is most likely because we have a 'mix', 'join', or 'group' operator somewhere and the pipeline needs to make sure the binning has completed to ensure it has mixed/joined everything before it can continue
James Fellows Yates
11/03/2025, 9:04 AMThere is a lot of 'manipulation' of Nextflow channels going on so it can be hard to say 😅 but if you want a more concrete answer feel free to ask #CE9MS66BS and maybe someone can do a deep dive
t
Thomas Haverkamp
11/03/2025, 9:51 AMOkay, than I understand it, than I just wait until my assemblies are done. They take time 😄