I download SortMeRNA from http://bioinfo.lifl.fr/RNA/sortmerna/. However, when I do
./configure make
I got error:
src/paralleltraversal.cpp:18:10: fatal error: 'omp.h' file not found #include^ 1 error generated.
Then I tried to use a different gcc.
Do:
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 make sudo make install
And I got:
qiuworld$ which sortmerna /usr/local/bin/sortmerna qiuworld$ sortmerna --version SortMeRNA version 1.9, 30/08/2013 30/08/2013 - fixed bug for naming output log file - modified merge-paired-reads.sh to work on a cluster 13/05/2013 - fixed bug to detect last (rRNA) read in fastq file - modified merge/unmerge-paired-reads.sh 05/04/2013 - changed to the usual 'configure, make, make install' (see the user manual v1.7) - added 'merge-paired-reads.sh' and 'unmerge-paired-reads.sh' 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
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.
thank you for your message. I will try that soon.