Question: Issues with STAR aligner install
0
gravatar for leonmcswain
4 months ago by
leonmcswain10
leonmcswain10 wrote:

I am running into some issues installing STAR aligner. I attempted to follow others solutions. Ive re-installed gcc thinking this was the issue while compiling but I am still getting an error:

leonfoymcswain@Leons-MBP ~ % cd ~/Desktop/Bio_Packages/STAR/source
leonfoymcswain@Leons-MBP source % make STARforMacStatic CXX=/usr/local/Cellar/gcc/8.2.0/bin/g++-8
/usr/local/Cellar/gcc/8.2.0/bin/g++-8 -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 20 22:06:48 EDT 2020 :/Users/leonfoymcswain/Desktop/Bio_Packages/STAR/source"' -D'COMPILE_FOR_MAC' -pipe -Wall -Wextra soloInputFeatureUMI.cpp
make: /usr/local/Cellar/gcc/8.2.0/bin/g++-8: No such file or directory
make: *** [soloInputFeatureUMI.o] Error 1
leonfoymcswain@Leons-MBP source % STAR
zsh: permission denied: STAR
leonfoymcswain@Leons-MBP source %

This was the second time I tried this so it doesn't show the entire output from the first attempt (looked like it basically finished compiling and then gave an error). Even if I set the PATH to the STAR unix executable file I still get permission denied. I have also tried sudo chmod to give permissions and again permission denied. Clearly a novice, any help would be great.

rna-seq star alignment • 234 views
ADD COMMENTlink modified 4 months ago by h.mon31k • written 4 months ago by leonmcswain10
1

what do you get when you type which g++-8 on your machine? Also, where did you obtain the file? Did you get it from github? https://github.com/alexdobin/STAR

I've looked into the makefile in the github and see that it simply uses the g++ on your machine. So if your which g++ come back with something sensible, using the github version should work.

ADD REPLYlink written 4 months ago by Sam3.3k

When I type which g++ I get usr/bin/g++ if I type which g++-8 I don't get anything. I used git clone to clone STAR through the terminal onto a file on my desktop (running this on mac). When I check the path (I realize the way I've done it below is not efficient) I find the gcc version is 10.1.0 and I think I need version 8.2.0? How would I install a specific version of gcc? Assuming this needs to be done through homebrew.

leonfoymcswain@Leons-MBP gcc % ls 10.1.0 leonfoymcswain@Leons-MBP gcc % cd 10.1.0 leonfoymcswain@Leons-MBP 10.1.0 % cd bin leonfoymcswain@Leons-MBP bin % ls
c++-10 gfortran-10 cpp-10 lto-dump-10 g++-10 x86_64-apple-darwin19-c++-10 gcc-10 x86_64-apple-darwin19-g++-10 gcc-ar-10 x86_64-apple-darwin19-gcc-10 gcc-nm-10 x86_64-apple-darwin19-gcc-10.1.0 gcc-ranlib-10 x86_64-apple-darwin19-gcc-ar-10 gcov-10 x86_64-apple-darwin19-gcc-nm-10 gcov-dump-10 x86_64-apple-darwin19-gcc-ranlib-10 gcov-tool-10 x86_64-apple-darwin19-gfortran-10 gfortran leonfoymcswain@Leons-MBP bin %

ADD REPLYlink modified 4 months ago • written 4 months ago by leonmcswain10

I found a solution. I uninstalled all gcc compilers other than gcc@8 and then changed the make directory to match the gcc@8 and it worked.

ADD REPLYlink written 4 months ago by leonmcswain10

This came at the end when compiling was finished and I am not sure if its significant or not.

Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:25:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered] for (uint imate=0;imate<readfilesnames.size();imate++) {="" open="" readin="" files="" ^~~~~<="" p="">

ld: warning: direct access in function 'operator new(unsigned long, std::nothrow_t const&) [clone .cold.0]' from file '/usr/local/Cellar/gcc@8/8.4.0_1/lib/gcc/8/gcc/x86_64-apple-darwin19/8.4.0/../../../libstdc++.a(new_opnt.o)' to global weak symbol 'operator new(unsigned long, std::nothrow_t const&)' from file '/usr/local/Cellar/gcc@8/8.4.0_1/lib/gcc/8/gcc/x86_64-apple-darwin19/8.4.0/../../../libstdc++.a(new_opnt.o)' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.

ADD REPLYlink modified 4 months ago • written 4 months ago by leonmcswain10

actually, using gcc 10.1.0 is ok, so you don't need to remove your gcc installation.

As for your last question. Maybe you can do a make clean or to clean the directory and redo the compilation. This should ensure that all your files are compiled by the same compiler. Should worth a try anyway.

ADD REPLYlink written 4 months ago by Sam3.3k

How do I remove the compiled files to "clean"? When I delete the STAR file and reinstall followed by compiling it shows compiled files like the files were never deleted.

ADD REPLYlink written 4 months ago by leonmcswain10

rm *.o in your build directory usually does the trick (unless there are some underlying structure)

ADD REPLYlink written 4 months ago by Sam3.3k
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