dg520
commented
5 years ago Hi @aart127 ,
I'm sorry to reply this late. I was finalizing a paper in the previous two weeks.
You encountered two MAC specific problems here:
1) When you run IRFinder with pre-compiled binaries, readlink on MAC does not support -f option.
2) When you tried to re-compile from source, the MAC default compiler clang LLVM does not support openmp. And in your case, you're still using clang instead of GCC 9.1.0 to compile. Please note, you do want to keep the default compiler to make other MAC software installation safe and easy.
The work around can be tricky on MAC OS. Among those, I recommend you to use a virtual environment. This makes your main system and environment is untouched if things did not work out eventually. If you're already using or familiar with conda or anaconda, the solution is more or less straightforward:
1) create a new conda environment for IRFinder and switch to that environment.
2) use conda install to install gcc and llvm.
3) compile IRFinder under this conda environment.
4) try to run IRFinder now. If it worked, remember to run IRFinder under this environment every time.
Let me know how it works. Apologize for the inconvenience. We didn't expect to run IRFinder on MAC or Windows.
Best, Dadi
Hi there. Please could you help with an issue calling IRFinder in bam mode?
Mac Mojave 10.14.5 gcc (Homebrew GCC 9.1.0) 9.1.0 bedtools v2.28.0
The reference was built under BuildRefProcess mode
server:bin roger$ ./IRFinder -t 1 -M 1000 -m BAM -r /Users/roger/Applications/IRFinder-1.2.5/REF/Human-hg19-release75 -d pooled_SL ~/Desktop/X4SL_unsorted.bam readlink: illegal option -- f usage: readlink [-n] [file ...] ./IRFinder: line 193: /proc/meminfo: No such file or directory ./IRFinder: line 194: /1000: syntax error: operand expected (error token is "/1000") ERROR: IRFinder appears not to have completed. It appears an unknown component crashed. ERROR: IRFinder appears not to have completed. It appears an unknown component crashed. ERROR: IRFinder appears not to have completed. It appears an unknown component crashed.
irfinder.stderr ./IRFinder: line 550: ./util/irfinder: cannot execute binary file
irfinder.stdout IRFinder version: 1.2.4 IRFinder start: Tue Jun 11 11:54:14 BST 2019 IRFinder runmode: BAM IRFinder user@host: roger @ server.pvrg.private IRFinder working dir: /Users/roger/Applications/IRFinder-1.2.5/bin IRFinder reference: /Users/roger/Applications/IRFinder-1.2.5/REF/Human-hg19-release75 IRFinder file 1: /Users/roger/Desktop/X4SL_unsorted.bam IRFinder file 2:
I've tried recompiling in src but get the following error: server:irfinder roger$ make hostname: illegal option -- - usage: hostname [-fs] [name-of-host] g++ -c -pipe -std=c++0x -O3 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Jun 2019 12:25:57 BST :/Users/roger/Applications/IRFinder-1.2.5/src/irfinder"' FragmentBlocks.cpp clang: error: unsupported option '-fopenmp' make: *** [FragmentBlocks.o] Error 1
Sorry if this is something obvious - I'm new to this...