无法在 Apple M1 上为 BWA 运行 make 命令（在 Mac OS Big Sur 上）答案

【问题标题】：Unable to run make command for BWA on Apple M1 (On Mac OS Big Sur)无法在 Apple M1 上为 BWA 运行 make 命令（在 Mac OS Big Sur 上）
【发布时间】：2021-04-09 19:16:15
【问题描述】：

我正在尝试使用 make 文件安装 BWA。 Github 仓库如下：

https://github.com/lh3/bwa

make文件如下：

CC=         gcc
#CC=            clang --analyze
CFLAGS=     -g -Wall -Wno-unused-function -O2
WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
AR=         ar
DFLAGS=     -DHAVE_PTHREAD $(WRAP_MALLOC)
LOBJS=      utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
            QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
AOBJS=      bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
            bwape.o kopen.o pemerge.o maxk.o \
            bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
            bwtsw2_chain.o fastmap.o bwtsw2_pair.o
PROG=       bwa
INCLUDES=   
LIBS=       -lm -lz -lpthread
SUBDIRS=    .

ifeq ($(shell uname -s),Linux)
    LIBS += -lrt
endif

.SUFFIXES:.c .o .cc

.c.o:
        $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

all:$(PROG)

bwa:libbwa.a $(AOBJS) main.o
        $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)

bwamem-lite:libbwa.a example.o
        $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)

libbwa.a:$(LOBJS)
        $(AR) -csru $@ $(LOBJS)

clean:
        rm -f gmon.out *.o a.out $(PROG) *~ *.a

depend:
    ( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )

# DO NOT DELETE THIS LINE -- make depend depends on it.

QSufSort.o: QSufSort.h
bamlite.o: bamlite.h malloc_wrap.h
bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h khash.h
bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kstring.h malloc_wrap.h kvec.h
bwa.o: kseq.h
bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h
bwamem.o: ksort.h utils.h kbtree.h
bwamem_extra.o: bwa.h bntseq.h bwt.h bwamem.h kstring.h malloc_wrap.h
bwamem_pair.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h kvec.h
bwamem_pair.o: utils.h ksw.h
bwape.o: bwtaln.h bwt.h kvec.h malloc_wrap.h bntseq.h utils.h bwase.h bwa.h
bwape.o: ksw.h khash.h
bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h malloc_wrap.h
bwase.o: bwa.h ksw.h
bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h
bwashm.o: bwa.h bntseq.h bwt.h
bwt.o: utils.h bwt.h kvec.h malloc_wrap.h
bwt_gen.o: QSufSort.h malloc_wrap.h
bwt_lite.o: bwt_lite.h malloc_wrap.h
bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h
bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h
bwtindex.o: bntseq.h bwa.h bwt.h utils.h rle.h rope.h malloc_wrap.h
bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h
bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h
bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h
bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h malloc_wrap.h
bwtsw2_core.o: khash.h ksort.h
bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h
bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h
bwtsw2_pair.o: malloc_wrap.h ksw.h
example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h
fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h
is.o: malloc_wrap.h
kopen.o: malloc_wrap.h
kstring.o: kstring.h malloc_wrap.h
ksw.o: ksw.h malloc_wrap.h
main.o: kstring.h malloc_wrap.h utils.h
malloc_wrap.o: malloc_wrap.h
maxk.o: bwa.h bntseq.h bwt.h bwamem.h kseq.h malloc_wrap.h
pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h
rle.o: rle.h
rope.o: rle.h rope.h
utils.o: utils.h ksort.h malloc_wrap.h kseq.h

但我收到以下错误。你能告诉我该怎么做吗？我在我的 macbook 中使用新的 Apply m1 芯片处理器。我尝试将 CC = 更改为 clang 并改回 gcc，在这两种情况下它都给出了相同的错误。

    gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
In file included from ksw.c:29:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/emmintrin.h:13:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/xmmintrin.h:13:
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:50:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:129:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:159:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:189:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:216:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:239:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:260:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:287:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:310:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:331:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:352:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:373:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:394:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:416:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:439:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:461:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:483:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:504:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include/mmintrin.h:525:12: error: 
      invalid conversion between vector type '__m64' (vector of 1 'long long'
      value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [ksw.o] Error 1

【问题讨论】：

标签： gcc bioinformatics macos-big-sur

【解决方案1】：

我遇到了这个问题，发现这个问题与 M1 mac 编译 C 代码的方式有关。对于 bwa，此解决方案对我有用（本质上是交换编译器在此过程中使用的文件）

cd bwa/
sed -i -e 's/<emmintrin.h>/"sse2neon.h"/' ksw.c
wget https://gitlab.com/arm-hpc/packages/uploads/ca862a40906a0012de90ef7b3a98e49d/sse2neon.h
make clean all

我想这将适用于许多需要在使用前进行编译的生物信息学工具（Bowtie，STAR）。

【讨论】：

这对我有用

【解决方案2】：

您需要修补 BWA 以使用 NEON 而不是 SSE 指令进行 SIMD 操作。我已在以下位置提供二进制文件：https://github.com/smikkelsendk/bwa-for-arm/tree/master/bin

【讨论】：

您能提供更多信息吗？目前尚不清楚上面链接的二进制文件是什么/应该使用哪个。谢谢！