how to install SortMeRNA on mac os x 10.8.5

I download SortMeRNA from However, when I do


I got error:

src/paralleltraversal.cpp:18:10: fatal error: 'omp.h' file not found
1 error generated.

Then I tried to use a different gcc.

sudo port selfupdate
sudo port install gcc48
sudo port install openmpi

After that Do:

./configure CC=/opt/local/bin/gcc-mp-4.8 CXX=g++-mp-4.8
sudo make install

And I got:

qiuworld$ which sortmerna
qiuworld$ sortmerna --version

  SortMeRNA version 1.9, 30/08/2013

  30/08/2013 - fixed bug for naming output log file
             - modified to work on a cluster
  13/05/2013 - fixed bug to detect last (rRNA) read in fastq file
             - modified merge/ 
  05/04/2013 - changed to the usual 'configure, make, make install' (see the user manual v1.7) 
             - added '' and '' for 
               forward-reverse paired-end reads (see the user manual v1.7) 
             - fixed an integer overflow for mmap calculation for 32-bit
  26/02/2013 - changed sysconf library to sysctl for Mac OS
             - the sequence tag in the provided rRNA databases now follows the format:
               >[accession] [taxonomy] [length] 
  15/02/2013 - error for output of paired reads >1GB resolved
             - option -m added for specifying the amount of memory for loading reads
             - reads of length < L (default L=18) are automatically considered as non-rRNA
             - local timestamp added to --log statistics file
  06/02/2013 - reads up to 5000 nucleotides supported (Illumina or 454 technology)
             - AUTHORS file added to SortMeRNA directory
  24/01/2013 - L=20 error messages resolved 
             - I/O file checks modified 
             - Makefile updated for setting $SORTMERNADIR 
             - support for paired-end reads 
  04/01/2013 - input directory can be current without any path
  20/12/2012 - reads input files without an extension allowed

2 thoughts on “how to install SortMeRNA on mac os x 10.8.5

  1. Try the latest version v1.99 beta. The default gcc compiler on Mac does not support OpenMP. Now, if the default compiler is used, the user should only get warning messages. For OpenMP support, gcc compiler from macports works.


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