Hi,
I'm trying to install cd-hit on a Mac osX el Capitan, but I can't find what's going wrong neither in the forum neither in the readme file. Any help would be welcome. make
seems to go fine, and make openmp=no
too. But then I cannot use any cd-hit command. Thanks !
This is what I get :
$ make
g++ -DNO_OPENMP -O2 cdhit-common.c++ -c
g++ -DNO_OPENMP -O2 cdhit-utility.c++ -c
g++ -DNO_OPENMP -O2 cdhit.c++ -c
g++ -DNO_OPENMP -O2 cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
g++ -DNO_OPENMP -O2 cdhit-est.c++ -c
g++ -DNO_OPENMP -O2 cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
g++ -DNO_OPENMP -O2 cdhit-2d.c++ -c
g++ -DNO_OPENMP -O2 cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
g++ -DNO_OPENMP -O2 cdhit-est-2d.c++ -c
g++ -DNO_OPENMP -O2 cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
g++ -DNO_OPENMP -O2 cdhit-div.c++ -c
g++ -DNO_OPENMP -O2 cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
g++ -DNO_OPENMP -O2 cdhit-454.c++ -c
g++ -DNO_OPENMP -O2 cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
$ make openmp=no
make: Nothing to be done for `all'.
$ cd-hit -i all.fasta -o clusters -c 0.4 -n 2 -M 6000 -T 6
-bash: cd-hit: command not found
nothing is wrong with make. You just have to append the directory to your PATH ... http://www.linfo.org/path_env_var.html
How to do CD-HIT clustering for phylogeny analysis, my doubt is how it is working, if we see manual, it will show cd-hit -i input_reads.fasta -o output, but we will be having one fasta file from one organisms, so how it will cluster taking one fasta file, if input file is single fasta file, or do we have to merge all file into single file, if it si how to do it. or if we keep all fasta file in single directory, than what will be the command.