This is my first time using PhyloPhlAn 3. I used the command below to build a tree for about 30 genomes, and the program has been running for over six days without finishing. The log files stopped showing any new output after about one day. Is this behavior normal? I also checked the CPU usage and found that the CPU load has been gradually decreasing.
phylophlan \
-i input_references \\
-o output_references \\
-d phylophlan \\
-t a \\
-f references_config.cfg \\
--nproc 20 \\
--diversity low \\
--fast \\
--verbose 2>&1 |tee logs/phylophlan__Rr
