Unable to install bwa-0.7.17 on ubuntu 10.06 virtualbox machine.

Question

[ricfoz]

hello all, i am trying to install bwa in my ubuntu guest virtual-machine. i have already downloaded, extracted .bz2 file, untared the resulting file, and i am standing in the bwa-0.7.17 folder. as i type make i receive the next set of errors:

(sorry for the length, i just wanted to share the complete info on my issue)

@ricfoz-VirtualBox:~/Downloads/bwa-0.7.17$ make
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
ksw.c: In function ‘ksw_u8’:
ksw.c:131:7: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi]
  zero = _mm_set1_epi32(0);
       ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:649:1: error: inlining failed in call to always_inline ‘_mm_set1_epi8’: target specific option mismatch
 _mm_set1_epi8 (char __A)
 ^
ksw.c:136:8: error: called from here
  shift = _mm_set1_epi8(q->shift);
        ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:649:1: error: inlining failed in call to always_inline ‘_mm_set1_epi8’: target specific option mismatch
 _mm_set1_epi8 (char __A)
 ^
ksw.c:135:8: error: called from here
  e_ins = _mm_set1_epi8(_e_ins);
        ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:649:1: error: inlining failed in call to always_inline ‘_mm_set1_epi8’: target specific option mismatch
 _mm_set1_epi8 (char __A)
 ^
ksw.c:134:9: error: called from here
  oe_ins = _mm_set1_epi8(_o_ins + _e_ins);
         ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:649:1: error: inlining failed in call to always_inline ‘_mm_set1_epi8’: target specific option mismatch
 _mm_set1_epi8 (char __A)
 ^
ksw.c:133:8: error: called from here
  e_del = _mm_set1_epi8(_e_del);
        ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:649:1: error: inlining failed in call to always_inline ‘_mm_set1_epi8’: target specific option mismatch
 _mm_set1_epi8 (char __A)
 ^
ksw.c:132:9: error: called from here
  oe_del = _mm_set1_epi8(_o_del + _e_del);
         ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:637:1: error: inlining failed in call to always_inline ‘_mm_set1_epi32’: target specific option mismatch
 _mm_set1_epi32 (int __A)
 ^
ksw.c:131:7: error: called from here
  zero = _mm_set1_epi32(0);
       ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:708:1: error: inlining failed in call to always_inline ‘_mm_store_si128’: target specific option mismatch
 _mm_store_si128 (__m128i *__P, __m128i __B)
 ^
ksw.c:142:3: error: called from here
   _mm_store_si128(Hmax + i, zero);
   ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:708:1: error: inlining failed in call to always_inline ‘_mm_store_si128’: target specific option mismatch
 _mm_store_si128 (__m128i *__P, __m128i __B)
 ^
ksw.c:141:3: error: called from here
   _mm_store_si128(H0 + i, zero);
   ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:708:1: error: inlining failed in call to always_inline ‘_mm_store_si128’: target specific option mismatch
 _mm_store_si128 (__m128i *__P, __m128i __B)
 ^
ksw.c:140:3: error: called from here
   _mm_store_si128(E + i, zero);
   ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:1186:1: error: inlining failed in call to always_inline ‘_mm_slli_si128’: target specific option mismatch
 _mm_slli_si128 (__m128i __A, const int __N)
 ^
ksw.c:149:5: error: called from here
   h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> 
     ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:690:1: error: inlining failed in call to always_inline ‘_mm_load_si128’: target specific option mismatch
 _mm_load_si128 (__m128i const *__P)
 ^
ksw.c:148:5: error: called from here
   h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,
     ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:690:1: error: inlining failed in call to always_inline ‘_mm_load_si128’: target specific option mismatch
 _mm_load_si128 (__m128i const *__P)
 ^
ksw.c:174:6: error: called from here
    h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
      ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:1372:1: error: inlining failed in call to always_inline ‘_mm_max_epu8’: target specific option mismatch
 _mm_max_epu8 (__m128i __A, __m128i __B)
 ^
ksw.c:172:6: error: called from here
    f = _mm_max_epu8(f, t);
      ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:1095:1: error: inlining failed in call to always_inline ‘_mm_subs_epu8’: target specific option mismatch
 _mm_subs_epu8 (__m128i __A, __m128i __B)
        ^
ksw.c:191:3: note: in expansion of macro ‘__max_16’
   __max_16(imax, max); // imax is the maximum number in max
   ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:1180:1: error: inlining failed in call to always_inline ‘_mm_srli_si128’: target specific option mismatch
 _mm_srli_si128 (__m128i __A, const int __N)
 ^
ksw.c:119:10: error: called from here
   (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \
          ^
ksw.c:191:3: note: in expansion of macro ‘__max_16’
   __max_16(imax, max); // imax is the maximum number in max
   ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:708:1: error: inlining failed in call to always_inline ‘_mm_store_si128’: target specific option mismatch
 _mm_store_si128 (__m128i *__P, __m128i __B)
 ^
ksw.c:204:5: error: called from here
     _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
     ^
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/5/include/emmintrin.h:690:1: error: inlining failed in call to always_inline ‘_mm_load_si128’: target specific option mismatch
 _mm_load_si128 (__m128i const *__P)
 ^
ksw.c:204:5: error: called from here
     _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
     ^
Makefile:25: recipe for target 'ksw.o' failed
make: *** [ksw.o] Error 1
@ricfoz-VirtualBox:~/Downloads/bwa-0.7.17$

What am i missing, should i install anything?, i can't get the grip on what's going on here. Any help would be most apreciated.

[Devon Ryan]

Are you using a 32 bit host or guest?

[ricfoz]

As far as i know, i am on a 64 bit host. OS Win7, my virtual machine is running ubuntu 16.04, yet i have architecture i686, which i have read is supposed to be 32 bit. i have printed my cpu info running

$ lscpu

the pertinent info reads as follows:

Architecture: i686 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian

while running :

sudo lshw

i get the folowing about the virtual machine:

-virtualbox
description: Computer product: VirtualBox vendor: innotek GmbH version: 1.2 serial: 0 width: 32 bits capabilities: smbios-2.5 dmi-2.5 configuration: family=Virtual Machine uuid=20E9A8AE-D209-4789-BBB4

it strikes me that it returns "width: 32 bits", since on the settings configuration of my virtualbox, on the window with the description where the VM is run, it returns "ubuntu 64 bit VM"

i hope that helps on my query for a way to get bwa to run on my machine.

Answer 1

[colindaven]

I would recommend bioconda for this. It really makes installing software a piece of cake, and is itself very easy to install. Give it a go!

[ricfoz]

i thought that myself, but i haven't been able either. Unless i have been getting things wrong. Is bioconda the same, or a dependence of Anaconda package? , i know i can set a conda environment through Anaconda to install packages, but that hasn't worked, but i should ask you if bioconda is the same as running Anaconda, or not. If your answer is negative, y may search about how to run bioconda.

Thank you for the advice in advance