BWA make error on Macbook pro

[Suimye]

Hello. everyone
I downloaded the bwa version 5.7 and cannot compile it on Macbook Pro (10.6.3).
I challenged following steps.

• 1. tar -xvf bwa-0.5.7.tar.bz2
• 2. cd /bwa-0.5.7
• 3. sh autogen.sh
• 4. ./configure
• 5. make

On make command, I can not continue the installation.
I think The linker is complaining that it cannot find the math library. I am not sure why this may happen. One thing I tried to remove the "-m64" option on the CFLAG line in Makefile. But I could not remove this error.

Any idea what the problem on my pc ?

And error message desribed below(Here, I did not removed -m64 option).
------------------------------------------------------
gcc -Wall -m64 -fPIC -g -O2 -o bwa is.o bwtmisc.o bwtindex.o simple_dp.o bwape.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o main.o bwt_gen/libbwtgen.a libbwacore.a -lpthread -lz -lm
Undefined symbols:
"_egzclose", referenced from:
_bwa_index in bwtindex.o
_bwa_index in bwtindex.o
_bwa_stdsw in simple_dp.o
_bwa_stdsw in simple_dp.o
_bsw2_aln in bwtsw2_aux.o
_bwa_fa2pac in libbwacore.a(bntseq.o)
_bwa_seq_close in libbwacore.a(bwaseqio.o)
"_egzopen", referenced from:
_err_xzopen_core in libbwacore.a(utils.o)
"_egzread", referenced from:
_ks_getuntil in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_ks_getuntil in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_ks_getuntil in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_ks_getuntil in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
"_egzdopen", referenced from:
_err_xzopen_core in libbwacore.a(utils.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [bwa] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

[jiaco]

I just tried on a 10.6.3 macbook, with xtools or xcode or whatever installed, and this worked:

bash autogen.sh
make

made a fake sequence file and

./bwa index test.fnt

worked without complaint. Wonder what that configure step messed up. Heres my log:

lotus:bwa-0.5.7 jiaco$ bash autogen.sh 
autoreconf: Entering directory `.'
autoreconf: configure.in: not using Gettext
autoreconf: running: aclocal -I m4
autoreconf: configure.in: tracing
autoreconf: configure.in: not using Libtool
autoreconf: running: /usr/bin/autoconf
autoreconf: running: /usr/bin/autoheader
autoreconf: running: automake --add-missing --copy --no-force
configure.in:45: installing `./config.sub'
configure.in:9: installing `./missing'
configure.in:9: installing `./install-sh'
configure.in:45: installing `./config.guess'
bwt_gen/Makefile.am: installing `./depcomp'
autoreconf: Leaving directory `.'
lotus:bwa-0.5.7 jiaco$ make
make[1]: Nothing to be done for `lib'.
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwt_gen.c -o bwt_gen.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   utils.c -o utils.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwt.c -o bwt.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwtio.c -o bwtio.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwtaln.c -o bwtaln.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwtgap.c -o bwtgap.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   is.c -o is.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bntseq.c -o bntseq.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwtmisc.c -o bwtmisc.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwtindex.c -o bwtindex.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   stdaln.c -o stdaln.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   simple_dp.c -o simple_dp.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwaseqio.c -o bwaseqio.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwase.c -o bwase.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwape.c -o bwape.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   kstring.c -o kstring.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   cs2nt.c -o cs2nt.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwtsw2_core.c -o bwtsw2_core.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwt_lite.c -o bwt_lite.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD   main.c -o main.o
gcc -g -Wall -O2 -m64 -DHAVE_PTHREAD  utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen

[drio]

Hello. everyone

On make command, I can not continue the installation.
I think The linker is complaining that it cannot find the math library. I am not sure why this may happen. One thing I tried to remove the "-m64" option on the CFLAG line in Makefile. But I could not remove this error.

zlib doesn't seem to be there.
Do you have this files in your machine?

/usr/lib/libz.1.dylib
/usr/include/zlib.h

[Suimye]

jiaco and drio
Thanks your rapid replying.

I checked the above files
>Do you have this files in your machine?
/usr/lib/libz.1.dylib yes
/usr/include/zlib.h yes

I continue trying BWA install...

[Jon_Keats]

I've been able to get this working on my MacBook Pro and our workstation, see my introduction thread for the exact method. It should work pretty easily unless something is amiss with your OS install or Xcode install

[Suimye]

Thanks Jon,

I have already installed Xcode. Now, I retried to install Xcode from DVD.
Unfortunately, I could not get working BWA (similar error on make step). And now, I download new version of Xcode 3.2.2 from web.
Also, I checked your thread for start up instrucitons. It was very nice thread, I think :-).
Thanks, your suggestion. I will try more.

[drio]

I think something is ****ed up with your gcc installation.
Try to tell gcc where to get the libs and the includes:

From the bwa dir:

gcc -Wall -m64 -fPIC -g -O2 -o bwa is.o bwtmisc.o bwtindex.o simple_dp.o bwape.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o main.o bwt_gen/libbwtgen.a libbwacore.a -lpthread -lz -lm -I/usr/lib -L/usr/include

Good luck.

[Suimye]

Hi drio,
Very thanks. I add your suggesting last part ("-I/usr/lib -L/usr/include") and tell from the bwa dir.
And result shown here.

gcc -Wall -m64 -fPIC -g -O2 -o bwa is.o bwtmisc.o bwtindex.o simple_dp.o bwape.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o main.o bwt_gen/libbwtgen.a libbwacore.a -lpthread -lz -lm -I/usr/lib -L/usr/include
Undefined symbols:
"_egzclose", referenced from:
_bwa_index in bwtindex.o
_bwa_index in bwtindex.o
_bwa_stdsw in simple_dp.o
_bwa_stdsw in simple_dp.o
_bsw2_aln in bwtsw2_aux.o
_bwa_fa2pac in libbwacore.a(bntseq.o)
_bwa_seq_close in libbwacore.a(bwaseqio.o)
"_egzopen", referenced from:
_err_xzopen_core in libbwacore.a(utils.o)
"_egzread", referenced from:
_ks_getuntil in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_kseq_read in simple_dp.o
_ks_getuntil in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_bsw2_aln in bwtsw2_aux.o
_ks_getuntil in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_bns_fasta2bntseq in libbwacore.a(bntseq.o)
_ks_getuntil in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
_bwa_read_seq in libbwacore.a(bwaseqio.o)
"_egzdopen", referenced from:
_err_xzopen_core in libbwacore.a(utils.o)
ld: symbol(s) not found

[dawe]

Hi drio,
Very thanks. I add your suggesting last part ("-I/usr/lib -L/usr/include")

Actually it's quite the opposite

-I/usr/include -L/usr/lib

BTW this is quite useless as those are default search paths. You are not missing or failing to link some system library. I believe the autogen tools forgot to generate the makefile part for some bwa object file. Just untar the archive and issue make.

$ tar xvjf bwa-0.5.7.tar.bz2
$ cd !$
$ make

[s-ikeda]

Hi

Did you install EMBOSS in your PC?
if you did it, you need to uninstall EMBOSS for making BWA.

http://sourceforge.net/mailarchive/forum.php?thread_name=D414B9BC-9D64-4CD4-90B9-F5ED543C931E%40sci.hokudai.ac.jp&forum_name=bio-bwa-help

[Suimye]

Thanks Ikeda,

I installed EMBOSS packages on my PC.
I resolved this problem by using making binary file from another my Mac.
But it is good replying for me.

Suimye

[drio]

He is asking you to remove those packages, not to install them.
Can you remove them and see if you can build bwa?

[Suimye]

Hi drio, (and to Ikeda)

Sorry, my replying make misreading.

I say YES for this ikeda's question.

But Im sorry, I can not remove it now.
Because now I use it .
After this problem, I was rescued by using making binary file from my another mac.
My another mac (OS-X leolard not installed EMBOSS packages) could install it.
Next time, I will try to install it after the uninstalling the EMBOSS packages on my mac book pro.


Thanks
Suimye

[vipo]

Hi,

I had the same problem, and did not need to deinstall EMBOSS. So I did the following, I downloaded the latest version of zlib (1.2.5) and installed it like the following:

cd zlib-1.2.5
./configure
make
make install
./configure --shared
make
make install

this installed the zlibs under /usr/local/libs, and just to be save I made made a symbolic link to the old (1.2.3) version in /usr/lib/

sudo ln -s /usr/local/lib/libz.1.2.5.dylib /usr/lib/libz.1.2.3.dylib

afterwards I recompiled bwa with

make clean
make

and it worked fine for me. Make sure that you make backups of the libs before modifying/updating them.

Cheers

[Suimye]

Hi vipo,
Thank you for your reply.
Installation was successful!
And also thanks to everyone who replied to me in this thread.