BWA installation problems

[seq_GA]

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

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

./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.

[sperry]

Try running 'sh ./autogen.sh'. This should create the configure script for you, so long as you have the GNU autotools package installed.

cd bwa-0.5.6
sh ./autogen.sh
./configure
make

This works for me in Ubuntu 9.10 (64bit)

-Scott

[lh3]

Just type "make" and copy the "bwa" binary anywhere you want.

[seq_GA]

Thanks Li. It works.

[zxl124]

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.

[lh3]

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.

[xl1]

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

[Amorvincit]

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?

[adaptivegenome]

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.

[aurinko]

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

[Amorvincit]

Thanks! bwa-0.6.0. install problem resolved

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) :-)

[angelinasusan]

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

[hakattack]

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

[Richard Finney]

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

[angelinasusan]

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