NGS exome FAQs

[kamilo889]

Hi all, I'm new in exome data analysis and I have few question and an Issue installing BWA-0.7.10.

1: Is necessary create a perl script to run the program since the first alignment to HG19 using bwa? or in the terminal I can work in a easier way?

2. Im triying to install BWA last version but when i run the command make appear a big mistake

camilo@camilo-G31M-S2L:~/bwa-0.7.10$ make
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
In file included from ksw.c:29:0:
/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:49:2: error: unknown type name ‘__m128i’
__m128i *qp, *H0, *H1, *E, *Hmax;
^
ksw.c: In function ‘ksw_qinit’:
ksw.c:72:11: error: ‘__m128i’ undeclared (first use in this function)
q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory

ksw.c:293:5: 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

Any idea?.
thanks a lot

[Bukowski]

1) No you can run things from the command line if you desire.

2) You're on a 32bit machine (i686). SSE2 instruction sets are implemented on 64bit processors.

You can run an old version of bwa on this type of hardware, 0.5x would be fine.

You'll not really be able to work on hg19 on a 32bit machine.

Source: http://sourceforge.net/p/bio-bwa/[email protected]/

[kamilo889]

Dear Bukowski thanks lot for your reply. about the first question ... what do you recommend? however, if I create a Perl file with my program is necessary install all the programs at first step right?.
About the second, you think that is better install 64bit version?

thanks again

[Bukowski]

At some point you will want to sequence your analysis workflow and how you do this is up to you - Perl, bash, Python, Makefiles - whatever you like, it's up to you. And yes you need to have all the programs installed first.

To do any kind of meaningful NGS analysis with human samples you need to be working on a 64bit *operating system* with 64bit *binaries* for your applications. Many apps, especially aligners are dropping 32bit support.

[GenoMax]

If you don't have access to a 64-bit machine then this change should allow you to compile bwa for 32-bit. Limits mentioned by Bukowski remain though. If you are working with human data then don't do this.

https://www.biostars.org/p/80351/