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Old 02-23-2010, 12:24 AM   #1
seq_GA
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Default BWA installation problems

After downloading bwa-0.5.6.tar.bz2, I used the following command to untar.

Code:
tar -xvf bwa-0.5.6.tar.bz2 
cd bwa-0.5.6
The INSTALL documents require us to r un the following three commands to install

Code:
./configure; 
make;
 make install'
But there are no ./configure command available. Only configure.in and config.h.in are available. Hence I started with the second command "make".

Can anyone tell me the steps involved in installation? Thanks.
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Old 02-23-2010, 05:31 AM   #2
sperry
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Try running 'sh ./autogen.sh'. This should create the configure script for you, so long as you have the GNU autotools package installed.

Code:
cd bwa-0.5.6
sh ./autogen.sh
./configure
make
This works for me in Ubuntu 9.10 (64bit)

-Scott
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Old 02-23-2010, 06:13 AM   #3
lh3
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Just type "make" and copy the "bwa" binary anywhere you want.
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Old 02-23-2010, 07:33 PM   #4
seq_GA
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Thanks Li. It works.
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Old 02-24-2010, 09:11 AM   #5
zxl124
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Quote:
Originally Posted by lh3 View Post
Just type "make" and copy the "bwa" binary anywhere you want.
I have another bwa installation problem. I installed bwa on 3 different Mac.
One is a 64 bit intel dual-core. I did what you said here, it runs just fine.
The second one is a PowerMac G5 dual-core 32bit. There was an error if I just type "make". So I edited two places in Makefile, changing 64 to 32. It worked and bwa runs fine.
The third one is a PowerMac G5 single core 32bit. Again I did the same thing as the other 32 bit Mac. "make" runs through without error message. However, when I tried to run "bwa aln ...". It sends an error message "calculate SA coordinates: Segmentation fault" and quits.

Any idea how to fix this?
Thanks.
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Old 02-24-2010, 10:45 AM   #6
lh3
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It is possible that bwa does not work on a big-endian CPU (x86 is little-endian while powerpc is big-endian). I have not tried.
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Old 07-28-2011, 08:58 AM   #7
xl1
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Default Segmentation fault - installation problem of BWA?

Hi,

Am I facing the installation problem of bwa-0.5.9rc1, as I am getting the following error:

[bwa_index] Pack FASTA... 68.61 sec
[bwa_index] Reverse the packed sequence... 20.18 sec
[bwa_index] Construct BWT for the packed sequence...
/ebi/lsf/ebi-spool/1311867442.7388100: line 8: 11897 Segmentation fault (core dumped) bwa index /net/isilon7/nobackup/services/embl/dist/xin/cram/Mus_musculus.NCBIM37.63.dna.toplevel.fa > /net/isilon7/nobackup/services/embl/dist/xin/cram/Mus_musculus.NCBIM37.63.dna.toplevel.fa.index
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Old 11-21-2011, 08:49 AM   #8
Amorvincit
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Default Similar (?) iMAC BWA install difficulties

Snowlion (10.6.8)
Downloaded bwa-0.6.0.tar.bz2 (129.9 kB)

./configure generates the error "No such file or directory"
as does sh: ./autogen.sh (not sure whether there is a Mac equivalent of this GNU Libtool?)

and make throws the following errors:

gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
bntseq.c: In function ‘bwa_fa2pac’:
bntseq.c:275: warning: implicit declaration of function ‘getopt’
bntseq.c:280: error: ‘optind’ undeclared (first use in this function)
bntseq.c:280: error: (Each undeclared identifier is reported only once
bntseq.c:280: error: for each function it appears in.)

and doesn't compile. Can anyone offer any advice?
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Old 11-21-2011, 09:54 AM   #9
adaptivegenome
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Did you run "sh: ./autogen.sh"? If so, you should remove the ":". I use BWA on Intel Macs and it runs fine. Let me know if you have more trouble.
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Old 11-22-2011, 01:13 AM   #10
aurinko
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As mentioned in the bio-bwa-help mailing list:

put "#include <unistd.h>" at the beginning of "bntseq.c"

After that use only "make" and all should be fine
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Old 11-24-2011, 03:54 AM   #11
Amorvincit
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Smile Thanks! bwa-0.6.0. install problem resolved

Quote:
Originally Posted by aurinko View Post
As mentioned in the bio-bwa-help mailing list:

put "#include <unistd.h>" at the beginning of "bntseq.c"

After that use only "make" and all should be fine
The include resolved it. Thanks (also to Genericforms) :-)
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Old 12-06-2012, 01:24 AM   #12
angelinasusan
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I'm trying to install bwa on biolinux and i get the following error during compilation using 'make'. Please help.
endocrinology@ubuntu:~/Downloads/bwa-0.6.2$ make
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwa.c -o bwa.o
In file included from bwa.c:8:0:
bntseq.h:32:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make: *** [bwa.o] Error 1
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Old 01-24-2013, 08:41 AM   #13
hakattack
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Default error compiling bwa.0.6.2 in linux

Has any one get this resolved please? i am trying to install bwa.0.6.2 in linux and here is what i am getting..

gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwa.c -o bwa.o
In file included from bwa.c:8:0:
bntseq.h:32:18: fatal error: zlib.h: No such file or directory

I would appreciate if someone can tell me what is going on.

Thanks
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Old 01-24-2013, 08:50 AM   #14
Richard Finney
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You need to point to libz.a or libz.so (zlib library file name).

See this thread ...
http://seqanswers.com/forums/showthread.php?t=3218
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Old 03-29-2013, 09:56 PM   #15
angelinasusan
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Default can someone help me fix this error?

when I try make after installation I get the following error:
gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD ksw.c -o ksw.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o
bwt.c: In function ‘bwt_restore_bwt’:
bwt.c:408:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwt.c:409:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwt.c:410:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwt.c: In function ‘bwt_restore_sa’:
bwt.c:382:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwt.c:384:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwt.c:385:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwt.c:386:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwt.c:393:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o
bntseq.c: In function ‘bns_restore_core’:
bntseq.c:98:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
bntseq.c:106:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
bntseq.c:114:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
bntseq.c:123:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
bntseq.c:129:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwa.c -o bwa.o
bwa.c: In function ‘bwa_idx_load’:
bwa.c:261:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwamem.c -o bwamem.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o
ar -csru libbwa.a utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
bwt_gen.c:873:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function ‘BWTIncMergeBwt’:
bwt_gen.c:947:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
bwt_gen.c: In function ‘BWTIncConstructFromPacked’:
bwt_gen.c:1452:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwt_gen.c:1468:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwt_gen.c:1483:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o
bwase.c: In function ‘bwa_sai2sam_se_core’:
bwase.c:516:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwase.c:530:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwase.c:535:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwase.c: In function ‘bwa_refine_gapped’:
bwase.c:309:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o
bwtindex.c: In function ‘bwt_pac2bwt’:
bwtindex.c:73:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwtindex.c: In function ‘bwa_seq_len’:
bwtindex.c:52:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o
bwape.c: In function ‘bwa_sai2sam_pe_core’:
bwape.c:642:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwape.c:645:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwape.c:653:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwape.c: In function ‘bwa_paired_sw’:
bwape.c:497:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwape.c: In function ‘bwa_cal_pac_pos_pe’:
bwape.c:278:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bwape.c:282:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -DHAVE_PTHREAD kopen.c -o kopen.o
kopen.c: In function ‘kopen’:
kopen.c:265:8: warning: ignoring return value of ‘pipe’, declared with attribute warn_unused_result [-Wunused-result]
kopen.c: In function ‘http_open’:
kopen.c:93:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
kopen.c: In function ‘kftp_send_cmd’:
kopen.c:146:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -DHAVE_PTHREAD pemerge.c -o pemerge.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
bwtsw2_aux.c: In function ‘bsw2_aln’:
bwtsw2_aux.c:738:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD fastmap.c -o fastmap.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o
gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o
gcc -g -Wall -O2 -DHAVE_PTHREAD QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread
gcc -c -g -Wall -O2 -DHAVE_PTHREAD example.c -o example.o
gcc -g -Wall -O2 -DHAVE_PTHREAD example.o -o bwamem-lite -L. -lbwa -lm -lz -lpthread
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Old 04-21-2015, 12:30 PM   #16
a.vhd
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Hi,
I have problem with bwa installation:
after typing make it running in to the following error:
Quote:
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
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Old 04-21-2015, 03:50 PM   #17
Richard Finney
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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
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Old 04-27-2015, 09:14 AM   #18
a.vhd
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Quote:
Originally Posted by Richard Finney View Post
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
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Old 04-27-2015, 09:59 AM   #19
GenoMax
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Quote:
Originally Posted by a.vhd View Post
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/
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Old 04-28-2015, 12:16 AM   #20
a.vhd
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Quote:
Originally Posted by GenoMax View Post
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?
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