BWA 'make' error

yasu · 02-15-2010, 06:37 PM

I just want to use BWA-0.5.6 for mapping 454 reads on Linux. I got error message like this;

=========
$ make
make[1]: Entering directory `/home/yago/bwa-0.5.6'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/yago/bwa-0.5.6'
make[1]: Entering directory `/home/yago/bwa-0.5.6/bwt_gen'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/yago/bwa-0.5.6/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD utils.c -o utils.o
utils.c:32:18: error: zlib.h: No such file or directory
In file included from utils.c:33:
utils.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’
utils.c:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’
make: *** [utils.o] Error 1
=========

Any suggestions? Thanks a lot!

drio · 02-15-2010, 07:48 PM

Quote:

Originally Posted by yasu

I just want to use BWA-0.5.6 for mapping 454 reads on Linux. I got error message like this;

=========
$ make
make[1]: Entering directory `/home/yago/bwa-0.5.6'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/yago/bwa-0.5.6'
make[1]: Entering directory `/home/yago/bwa-0.5.6/bwt_gen'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/yago/bwa-0.5.6/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD utils.c -o utils.o
utils.c:32:18: error: zlib.h: No such file or directory
In file included from utils.c:33:
utils.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’
utils.c:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’
make: *** [utils.o] Error 1
=========

Any suggestions? Thanks a lot!

Install the zlib package (zlib and zlib-devel) in your linux distribution.

debian/ubuntu

$ sudo apt-get install zlib-dev

redhat/fedora

$ sudo yum install zlib-dev

yasu · 02-16-2010, 12:25 AM

Thanks, drio!!
'$ sudo yum install zlib-devel' DOES work!!

xujie · 12-23-2010, 04:55 AM

Thank you
that works

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02-15-2010, 06:37 PM	#1
yasu Member Location: Japan Join Date: Jul 2009 Posts: 10	BWA 'make' error I just want to use BWA-0.5.6 for mapping 454 reads on Linux. I got error message like this; ========= $ make make[1]: Entering directory `/home/yago/bwa-0.5.6' make[1]: Nothing to be done for `lib'. make[1]: Leaving directory `/home/yago/bwa-0.5.6' make[1]: Entering directory `/home/yago/bwa-0.5.6/bwt_gen' make[1]: Nothing to be done for `lib'. make[1]: Leaving directory `/home/yago/bwa-0.5.6/bwt_gen' gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD utils.c -o utils.o utils.c:32:18: error: zlib.h: No such file or directory In file included from utils.c:33: utils.h:46: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’ utils.c:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘err_xzopen_core’ make: *** [utils.o] Error 1 ========= Any suggestions? Thanks a lot!

02-16-2010, 12:25 AM	#3
yasu Member Location: Japan Join Date: Jul 2009 Posts: 10	Thanks, drio!! '$ sudo yum install zlib-devel' DOES work!!

12-23-2010, 04:55 AM	#4
xujie Member Location: China Join Date: Nov 2010 Posts: 11	Thank you that works