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alexdobin / STAR

RNA-seq aligner

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make STAR error and unable to install gcc using homebrew

mahek3012 opened this issue · comments

commented

So I'm analysing RNA-seq data of data available from NCBI and I'm very novice in this area. Im using Mac M1-arm 64 architecture. I have prepare pipeline for preprocessing of this dataset which contains 30 samples using SNAKEMAKE. I'm stuck in aligning the reads.

  1. Firstly I used bwa-mem for alignment, the rule was working but it was taking a lot of time. and when I went back to literature, I saw STAR is the best aligner tool for human genome.
  2. So, I used Miniconda and tried to install star. but it says there is no STAR package available. so I installed to my working directory and was trying to make STAR. but it threw this error:

(star) mahek@ snakemake-data % cd STAR-2.7.11b/source
(star) mahek@. source % make STAR-2.7.11b
date: illegal option -- -
usage: date [-jnRu] [-I[date|hours|minutes|seconds]] [-f input_fmt]
[-r filename|seconds] [-v[+|-]val[y|m|w|d|H|M|S]]
[[[[mm]dd]HH]MM[[cc]yy][.SS] | new_date] [+output_fmt]
make: *** No rule to make target `STAR-2.7.11b'. Stop.
(star) mahek@ source % make STAR
date: illegal option -- -
usage: date [-jnRu] [-I[date|hours|minutes|seconds]] [-f input_fmt]
[-r filename|seconds] [-v[+|-]val[y|m|w|d|H|M|S]]
[[[[mm]dd]HH]MM[[cc]yy][.SS] | new_date] [+output_fmt]
c++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE=" :/Users/mahek/snakemake-data/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -pipe -Wall -Wextra systemFunctions.cpp
clang: error: unsupported option '-fopenmp'
make: *** [systemFunctions.o] Error 1

Then I tried to download homebrew without sudo. and tried to follow the steps from the manual that I need gcc to install. but it threw me this error:
./configure --prefix=/Users/mahek/snakemake-data/STAR-2.7.11b/source/homebr
==> make
Last 15 lines from /Users/mahek/Library/Logs/Homebrew/gcc/02.make:
In file included from ../../gcc/system.h:233:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/vector:321:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__format/formatter_bool.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__format/formatter_integral.h:32:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/locale:202:
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/c++/v1/__locale:813:5: error: expected expression
return std::use_facet<ctype<_CharT> >(__loc).is(ctype_base::cntrl, __c);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[3]: *** [cp/module.o] Error 1
rm gcc.pod
make[2]: *** [all-stage1-gcc] Error 2
make[1]: *** [stage1-bubble] Error 2
make: *** [all] Error 2

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These open issues may also help:
gcc: error in catching C++ exceptions Homebrew/homebrew-core#162714
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