Hi,
I am wondering if it is true that now users are no longer able to put in a --min_read_depth option for the sample2markers.py? Is there any alternative to this except changing the sample2markers.py file itself in util (which is hard since I work on a shared cluster).
Thanks!
Annie
Hi @cusoiv
When developing version 3, we decided to simplify the procedure and only reconstruct sequences with at least 8 reads mapping. However, we are getting some similar requests and in the next minor release we will have that and other options available. Right now, the only way to change it is, as you said, modify the script in utils.
Best,
Aitor
Hi @cusoiv
I uploaded to the MetaPhlAn repository the modified version of the sample2markers.py script that accepts additional parameters for the consensus markers reconstruction MetaPhlAn/sample2markers.py at master · biobakery/MetaPhlAn · GitHub
While the conda installation is still not available with this version, you can clone the repo and install it via pip or just replace the old sample2markers.py script with the new one.
Best,
Aitor
Hi @aitor.blancomiguez ,
Many thanks for the fast response and the changes!! Will try it out 
Best,
Annie