I run the sample code in here: StrainPhlAn3 · biobakery/biobakery Wiki · GitHub
mkdir consensus_markers sample2markers.py -i sams_simplified/*.sam.bz2 -o consensus_markers --nproc 4
when it’s done (files are generated and would not change in size), the job continues to be active and does not end itself.
I use my own files altogether using the above script. same problem of not ending itself occurred. I then tried my files one by one in a loop, the loop is stuck after the first file is processed.