[a.vhd]

Hi,
I have problem with bwa installation:
after typing make it running in to the following error:

gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
In file included from ksw.c:28:0:
/usr/lib/gcc/i686-linux-gnu/4.8/include/emmintrin.h:31:3: error: #error "SSE2 instruction set not enabled"
# error "SSE2 instruction set not enabled"
^
ksw.c:48:2: error: unknown type name ‘__m128i’
__m128i *qp, *H0, *H1, *E, *Hmax;
^
ksw.c: In function ‘ksw_qinit’:
ksw.c:71:11: error: ‘__m128i’ undeclared (first use in this function)
q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory
^
ksw.c:71:11: note: each undeclared identifier is reported only once for each function it appears in
ksw.c:71:19: error: expected expression before ‘)’ token
q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory
^
ksw.c: In function ‘ksw_u8’:
ksw.c:114:2: error: unknown type name ‘__m128i’
__m128i zero, gapoe, gape, shift, *H0, *H1, *E, *Hmax;
^
ksw.c:130:2: warning: implicit declaration of function ‘_mm_set1_epi32’ [-Wimplicit-function-declaration]
zero = _mm_set1_epi32(0);
^
ksw.c:131:2: warning: implicit declaration of function ‘_mm_set1_epi8’ [-Wimplicit-function-declaration]
gapoe = _mm_set1_epi8(_gapo + _gape);
^
ksw.c:137:3: warning: implicit declaration of function ‘_mm_store_si128’ [-Wimplicit-function-declaration]
_mm_store_si128(E + i, zero);
^
ksw.c:144:3: error: unknown type name ‘__m128i’
__m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
^
ksw.c:145:3: warning: implicit declaration of function ‘_mm_load_si128’ [-Wimplicit-function-declaration]
h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
^
ksw.c:146:3: warning: implicit declaration of function ‘_mm_slli_si128’ [-Wimplicit-function-declaration]
h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian
^
ksw.c:154:4: warning: implicit declaration of function ‘_mm_adds_epu8’ [-Wimplicit-function-declaration]
h = _mm_adds_epu8(h, _mm_load_si128(S + j));
^
ksw.c:155:4: warning: implicit declaration of function ‘_mm_subs_epu8’ [-Wimplicit-function-declaration]
h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)
^
ksw.c:157:4: warning: implicit declaration of function ‘_mm_max_epu8’ [-Wimplicit-function-declaration]
h = _mm_max_epu8(h, e);
^
ksw.c:181:5: warning: implicit declaration of function ‘_mm_movemask_epi8’ [-Wimplicit-function-declaration]
cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero));
^
ksw.c:181:5: warning: implicit declaration of function ‘_mm_cmpeq_epi8’ [-Wimplicit-function-declaration]
ksw.c:187:3: warning: implicit declaration of function ‘_mm_srli_si128’ [-Wimplicit-function-declaration]
__max_16(imax, max); // imax is the maximum number in max
^
ksw.c:187:3: warning: implicit declaration of function ‘_mm_extract_epi16’ [-Wimplicit-function-declaration]
ksw.c: In function ‘ksw_i16’:
ksw.c:232:2: error: unknown type name ‘__m128i’
__m128i zero, gapoe, gape, *H0, *H1, *E, *Hmax;
^
ksw.c:248:2: warning: implicit declaration of function ‘_mm_set1_epi16’ [-Wimplicit-function-declaration]
gapoe = _mm_set1_epi16(_gapo + _gape);
^
ksw.c:260:3: error: unknown type name ‘__m128i’
__m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
^
ksw.c:264:4: warning: implicit declaration of function ‘_mm_adds_epi16’ [-Wimplicit-function-declaration]
h = _mm_adds_epi16(h, *S++);
^
ksw.c:266:4: warning: implicit declaration of function ‘_mm_max_epi16’ [-Wimplicit-function-declaration]
h = _mm_max_epi16(h, e);
^
ksw.c:270:4: warning: implicit declaration of function ‘_mm_subs_epu16’ [-Wimplicit-function-declaration]
h = _mm_subs_epu16(h, gapoe);
^
ksw.c:286:5: warning: implicit declaration of function ‘_mm_cmpgt_epi16’ [-Wimplicit-function-declaration]
if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
^
make: *** [ksw.o] Error 1

[Richard Finney]

What version of gcc do you have?
What type of machine are you on?
What version of bwa?
What does "uname -a" return on your command line? This should provide the machine architecture.


Check here : http://seqanswers.com/forums/showthr...1&goto=newpost
and here
http://stackoverflow.com/questions/9...et-not-enabled

[a.vhd]

What version of gcc do you have?
What type of machine are you on?
What version of bwa?
What does "uname -a" return on your command line? This should provide the machine architecture.


Check here : http://seqanswers.com/forums/showthr...1&goto=newpost
and here
http://stackoverflow.com/questions/9...et-not-enabled

Thanks for your responding,
gcc version: 4.8.2 (Ubuntu 4.8.2-19ubuntu1)
I install Ubuntu 14.04.2 LTS on WMware Workstation
Bwa version: bwa-0.7.5a
Uname –a: Linux ubuntu 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:45:15 UTC 2015 i686 i686 i686 GNU/Linux

[GenoMax]

Thanks for your responding,
gcc version: 4.8.2 (Ubuntu 4.8.2-19ubuntu1)
I install Ubuntu 14.04.2 LTS on WMware Workstation
Bwa version: bwa-0.7.5a
Uname –a: Linux ubuntu 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:45:15 UTC 2015 i686 i686 i686 GNU/Linux

You are using 32-bit Ubuntu. If possible consider installing 64-bit Ubuntu since you will run into memory limitations (specially with human genome size references) once you start doing data analysis.

If that is not feasible then use Pierre's suggestions in this thread to make necessary changes to get bwa to compile on 32-bit linux: https://www.biostars.org/p/80351/

[a.vhd]

You are using 32-bit Ubuntu. If possible consider installing 64-bit Ubuntu since you will run into memory limitations (specially with human genome size references) once you start doing data analysis.

If that is not feasible then use Pierre's suggestions in this thread to make necessary changes to get bwa to compile on 32-bit linux: https://www.biostars.org/p/80351/

Thanks a lot for your guidance,
I try "more Makefile" command and receive those outputs but the process stop on "--More--(20%)".When I want to close the terminal it shows There is still a process running!

Is it necessary to install 64-bit Ubuntu since I had some problems working with Trimmomatic too?

[GenoMax]

Thanks a lot for your guidance,
I try "more Makefile" command and receive those outputs but the process stop on "--More--(20%)".When I want to close the terminal it shows There is still a process running!

"more" command displays the content of the makefile (more program shows a screenful of information at one time, space bar takes you to next screenful and the key b will take you back one screen). You will need to use an editor (you can use a graphical text editor in ubuntu, if you find it easier) to make the changes to the makefile and then save those changes.

If you are not familiar with the command line/linux then this link has a good guide targeted towards biologists: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1

Is it necessary to install 64-bit Ubuntu since I had some problems working with Trimmomatic too?

Are you doing re-sequencing? What is the size of the reference genome you are working with? Like I said yesterday if it is > 1 Gbp then you should consider switching to 64-bit ubuntu as long as you have > 4 GB RAM in your computer.

[a.vhd]

"more" command displays the content of the makefile (more program shows a screenful of information at one time, space bar takes you to next screenful and the key b will take you back one screen). You will need to use an editor (you can use a graphical text editor in ubuntu, if you find it easier) to make the changes to the makefile and then save those changes.

What kind of changes do you mean?

Are you doing re-sequencing? What is the size of the reference genome you are working with? Like I said yesterday if it is > 1 Gbp then you should consider switching to 64-bit ubuntu as long as you have > 4 GB RAM in your computer

.

I 'm working on RNA-seq (Illumina), the size of them is about 7-12 GB

[GenoMax]

What kind of changes do you mean?

Your makefile has to look like this (only first few lines copied below, make any changes needed) before you can compile bwa on 32-bit Ubuntu.

Quoted from Pierre's suggestions from biostars thread linked above:

    CC=            gcc
    CFLAGS=        -g -Wall -O2 -msse -mmmx -msse2
    AR=            ar
    DFLAGS=        -DHAVE_PTHREAD
    LOBJS=        utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pai

I 'm working on RNA-seq (Illumina), the size of them is about 7-12 GB

What is the size of your reference genome (assuming this was a re-sequencing project)?