Installing mothur error

g++ -O3 -std=c++11 -pthread -DVERSION=“"1.48.0"” -DRELEASE_DATE=“"5/20/22"” -DUSE_READLINE -I. -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -c -o source/calculators/accuracy.o source/calculators/accuracy.cpp
In file included from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/accuracy.hpp:12,
from source/calculators/accuracy.cpp:9:
source/datastructures/datavector.hpp:4:10: fatal error: mothurout.h: No such file or directory
4 | #include “mothurout.h”
| ^~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:144: source/calculators/accuracy.o] Error 1

You might try to download the source code again and recompile. That file should be there.

Is there a reason you’re trying to build from source?


No, but just following the MiSeq sop … after all I reinstall it via sudo

You should probably be using the precompiled binaries that you can find at Release Version 1.48.0 · mothur/mothur · GitHub

I have another question can I use Mothur to analyze shotgun metagenomics data?
if yes! how can I do that?

It’s for amplicon sequence data. I’d encourage you to find a paper that uses shotgun metagenomics sequence analysis and use their methods.


Can I use Mothur to get ASVs?

Yes you can. If you look at the MiSeq SOP you’ll see a section on ASVs.