BWA: Can't get it to compile

[darshan]

I am not an advanced C user. Can't get BWA to compile on Ubuntu 9.04

:~/nextgen/tools/bwa-0.5.5$ make
make[1]: Entering directory `/csbiohome/darshan/nextgen/tools/bwa-0.5.5'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/csbiohome/darshan/nextgen/tools/bwa-0.5.5'
make[1]: Entering directory `/csbiohome/darshan/nextgen/tools/bwa-0.5.5/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function ‘BWTIncConstructFromPacked’:
bwt_gen.c:1416: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwt_gen.c:1432: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwt_gen.c:1447: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
make[1]: Leaving directory `/csbiohome/darshan/nextgen/tools/bwa-0.5.5/bwt_gen'
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
bwtio.c: In function ‘bwt_restore_sa’:
bwtio.c:36: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:38: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:39: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:40: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:47: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c: In function ‘bwt_restore_bwt’:
bwtio.c:62: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:63: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:64: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
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
bntseq.c: In function ‘bns_restore’:
bntseq.c:99: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:107: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:115: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:125: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:131: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
bwtmisc.c: In function ‘bwa_seq_len’:
bwtmisc.c:51: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwt_pac2bwt’:
bwtmisc.c:72: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwa_pac_rev_core’:
bwtmisc.c:171: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwa_pac2cspac_core’:
bwtmisc.c:209: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
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
bwase.c: In function ‘bwa_refine_gapped’:
bwase.c:235: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:241: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c: In function ‘bwa_sai2sam_se_core’:
bwase.c:432: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:444: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:449: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c: In function ‘bwa_print_all_hits’:
bwase.c:514: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:521: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:526: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwape.c -o bwape.o
bwape.c: In function ‘bwa_cal_pac_pos_pe’:
bwape.c:259: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c:263: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c: In function ‘bwa_paired_sw’:
bwape.c:446: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c: In function ‘bwa_sai2sam_pe_core’:
bwape.c:558: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c:559: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c:571: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
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
bwtsw2_aux.c: In function ‘bsw2_aln’:
bwtsw2_aux.c:606: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
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

[lh3]

These is no single error in compiling. Why do you say it cannot be compiled?

[darshan]

Its now resolved.
I was getting a file with a funny name as output and bwa executable was of 0 bytes

Now I did:
cd bwt_gen
make
cd ..
make

I suggest a section "how to install bwa" in the readme/documentation

[jjjscuedu]

HI all,

However, for my compile error is like this:

DO you know where is wrong? Thanks!

jingjing@ubuntu:~/BWA$ cd bwa-0.5.7/
jingjing@ubuntu:~/BWA/bwa-0.5.7$ make
make[1]: Entering directory `/home/jingjing/BWA/bwa-0.5.7'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/jingjing/BWA/bwa-0.5.7'
make[1]: Entering directory `/home/jingjing/BWA/bwa-0.5.7/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
In file included from /usr/include/features.h:387,
from /usr/include/stdio.h:28,
from bwt_gen.c:25:
/usr/include/gnu/stubs.h:9: fatal error: gnu/stubs-64.h: No such file or directory
compilation terminated.
make[1]: *** [bwt_gen.o] Error 1
make[1]: Leaving directory `/home/jingjing/BWA/bwa-0.5.7/bwt_gen'
make: *** [lib-recur] Error 1

[Richard Finney]

Try this ...

sudo apt-get install libc6-dev

and perhaps these ...

sudo apt-get install libc6-dev-amd64
sudo apt-get install libc6-dev-i386

[jjjscuedu]

Thanks very much!

However, I have installed these libraries. The result is still error like this:

root@ubuntu:/home/jingjing/BWA/bwa-0.5.7# make
make[1]: Entering directory `/home/jingjing/BWA/bwa-0.5.7'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/jingjing/BWA/bwa-0.5.7'
make[1]: Entering directory `/home/jingjing/BWA/bwa-0.5.7/bwt_gen'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/jingjing/BWA/bwa-0.5.7/bwt_gen'
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
bwtio.c: In function ‘bwt_restore_sa’:
bwtio.c:36: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:38: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:39: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:40: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:47: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c: In function ‘bwt_restore_bwt’:
bwtio.c:62: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:63: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:64: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
bwtaln.c: In function ‘bwa_aln’:
bwtaln.c:255: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result
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
bntseq.c: In function ‘bns_restore_core’:
bntseq.c:98: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:106: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:114: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:123: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:129: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o
bwtmisc.c: In function ‘bwa_seq_len’:
bwtmisc.c:51: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwt_pac2bwt’:
bwtmisc.c:72: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwa_pac_rev_core’:
bwtmisc.c:171: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwa_pac2cspac_core’:
bwtmisc.c:209: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
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
bwase.c: In function ‘bwa_refine_gapped’:
bwase.c:312: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:318: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c: In function ‘bwa_sai2sam_se_core’:
bwase.c:566: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:578: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:583: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c: In function ‘bwa_sai2sam_se’:
bwase.c:619: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwape.c -o bwape.o
bwape.c: In function ‘bwa_cal_pac_pos_pe’:
bwape.c:293: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c:297: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c: In function ‘bwa_paired_sw’:
bwape.c:497: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c: In function ‘bwa_sai2sam_pe_core’:
bwape.c:637: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c:638: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c:650: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c: In function ‘bwa_sai2sam_pe’:
bwape.c:722: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result
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
bwtsw2_main.c: In function ‘bwa_bwtsw2’:
bwtsw2_main.c:35: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o
bwtsw2_aux.c: In function ‘bsw2_aln’:
bwtsw2_aux.c:609: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
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
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i686-linux-gnu/4.4.5/../../../libz.so when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i686-linux-gnu/4.4.5/../../../libz.a when searching for -lz
/usr/bin/ld: skipping incompatible //usr/lib/libz.so when searching for -lz
/usr/bin/ld: skipping incompatible //usr/lib/libz.a when searching for -lz
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make: *** [bwa] Error 1

DO you know why? DO you need to install other libraries?

Thanks!

[Richard Finney]

It cant find zlib libarry

try:
apt-get install zlib1g zlib1g-dev

to install zlib

[jjjscuedu]

I have tried to install zlib. However, it seems this library has been installed.

When I try to compile the BWA again, the error is the same. Do you know it is because other errors?

Thanks!

Jingjing
root@ubuntu:/home/jingjing/BWA/bwa-0.5.7# apt-get install zlib1g zlib1g-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
zlib1g is already the newest version.
zlib1g-dev is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

[oigl]

Hi!
Maybe you would find useful compiled BWA which goes within the Ugene FULL package. Most BWA options are available from the Ugene GUI also, see http://ugene.unipro.ru/documentation...ort_reads.html

[Richard Finney]

The linker can not find zlib (known as file name libz.so or libz.a).
Your path to where libraries is not correct

What is the output of this command : ldconfig -p | grep libz

I get ...
libzipios.so.0 (libc6) => /usr/lib/libzipios.so.0
libzephyr.so.4 (libc6) => /usr/lib/libzephyr.so.4
libzeitgeist-1.0.so.1 (libc6) => /usr/lib/libzeitgeist-1.0.so.1
libzbar.so.0 (libc6) => /usr/lib/libzbar.so.0
libz.so.1 (libc6) => /lib/i386-linux-gnu/libz.so.1
libz.so (libc6) => /usr/lib/i386-linux-gnu/libz.so

To fix your problem
You can add a "--library-path=" option (or -L) to the
LIBS= ***ADD -L HERE **** -lm -lz -lpthread -Lbwt_gen -lbwtgen
line in bwa's Makefile

Another way to fix it is to run ldconfig ( check out this discussion : http://www.cyberciti.biz/tips/linux-...anagement.html ) to fix it. You'll need to get command parameters right.

[jjjscuedu]

HI,

THanks for your suggestions.

I have tried your method 1 like this:

jingjing@ubuntu:~$ ldconfig -p | grep libz
libzephyr.so.4 (libc6) => /usr/lib/libzephyr.so.4
libzbar.so.0 (libc6) => /usr/lib/libzbar.so.0
libz.so.1 (libc6) => /lib/libz.so.1
libz.so (libc6) => /usr/lib/libz.so

Then, I add the library path to the makefile of BWA like this:
LIBS= --library-path=usr/lib/libz.so -lm -lz -lpthread -Lbwt_gen -lbwtgen

HOwever, the result is still the same.

Jingjing

[Richard Finney]

Instead of
LIBS= --library-path=usr/lib/libz.so -lm -lz -lpthread -Lbwt_gen -lbwtgen

try
LIBS= --library-path=/usr/lib/libz.so -lm -lz -lpthread -Lbwt_gen -lbwtgen

[jjjscuedu]

Sorry, I copy wrong link about the library, I really use the:

LIBS= --library-path=/usr/lib/libz.so -lm -lz -lpthread -Lbwt_gen -lbwtgen

However, the error is still like this:

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 --library-path=/usr/lib/libz.so -lm -lz -lpthread -Lbwt_gen -lbwtgen
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i686-linux-gnu/4.4.5/../../../libz.so when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i686-linux-gnu/4.4.5/../../../libz.a when searching for -lz
/usr/bin/ld: skipping incompatible //usr/lib/libz.so when searching for -lz
/usr/bin/ld: skipping incompatible //usr/lib/libz.a when searching for -lz
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make: *** [bwa] Error 1