Burrows-Wheeler Alignment Tool Make Error

[jmwhitha]

Good morning,

I am having trouble with 'making' bwa. Below I posted my code and my error messages. Any help would be much appreciated.

My commands:
#gets the newest version from sourceforge
wget http://sourceforge.net/projects/bio-...r.bz2/download -O bwa.tar.bz2

#unpacks the tarball
tar -xjf bwa.tar.bz2
cd bwa-0.7.3a

#makes bwa
make

My errors:
jmwhitha@Linux-OptiPlex-755:~/bwa-0.7.3a$ make
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
In file included from ksw.c:28:0:
/usr/lib/gcc/i686-linux-gnu/4.7/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"
ksw.c:44:2: error: unknown type name ‘__m128i’
ksw.c: In function ‘ksw_qinit’:
ksw.c:67:11: error: ‘__m128i’ undeclared (first use in this function)
ksw.c:67:11: note: each undeclared identifier is reported only once for each function it appears in
ksw.c:67:19: error: expected expression before ‘)’ token
ksw.c: In function ‘ksw_u8’:
ksw.c:110:2: error: unknown type name ‘__m128i’
ksw.c:126:2: warning: implicit declaration of function ‘_mm_set1_epi32’ [-Wimplicit-function-declaration]
ksw.c:127:2: warning: implicit declaration of function ‘_mm_set1_epi8’ [-Wimplicit-function-declaration]
ksw.c:133:3: warning: implicit declaration of function ‘_mm_store_si128’ [-Wimplicit-function-declaration]
ksw.c:140:3: error: unknown type name ‘__m128i’
ksw.c:141:3: warning: implicit declaration of function ‘_mm_load_si128’ [-Wimplicit-function-declaration]
ksw.c:142:3: warning: implicit declaration of function ‘_mm_slli_si128’ [-Wimplicit-function-declaration]
ksw.c:150:4: warning: implicit declaration of function ‘_mm_adds_epu8’ [-Wimplicit-function-declaration]
ksw.c:151:4: warning: implicit declaration of function ‘_mm_subs_epu8’ [-Wimplicit-function-declaration]
ksw.c:153:4: warning: implicit declaration of function ‘_mm_max_epu8’ [-Wimplicit-function-declaration]
ksw.c:177:5: warning: implicit declaration of function ‘_mm_movemask_epi8’ [-Wimplicit-function-declaration]
ksw.c:177:5: warning: implicit declaration of function ‘_mm_cmpeq_epi8’ [-Wimplicit-function-declaration]
ksw.c:183:3: warning: implicit declaration of function ‘_mm_srli_si128’ [-Wimplicit-function-declaration]
ksw.c:183:3: warning: implicit declaration of function ‘_mm_extract_epi16’ [-Wimplicit-function-declaration]
ksw.c: In function ‘ksw_i16’:
ksw.c:227:2: error: unknown type name ‘__m128i’
ksw.c:243:2: warning: implicit declaration of function ‘_mm_set1_epi16’ [-Wimplicit-function-declaration]
ksw.c:255:3: error: unknown type name ‘__m128i’
ksw.c:259:4: warning: implicit declaration of function ‘_mm_adds_epi16’ [-Wimplicit-function-declaration]
ksw.c:261:4: warning: implicit declaration of function ‘_mm_max_epi16’ [-Wimplicit-function-declaration]
ksw.c:265:4: warning: implicit declaration of function ‘_mm_subs_epu16’ [-Wimplicit-function-declaration]
ksw.c:281:5: warning: implicit declaration of function ‘_mm_cmpgt_epi16’ [-Wimplicit-function-declaration]
make: *** [ksw.o] Error 1

Thank you and God bless,
Jason

[lh3]

The latest bwa requires SSE2. If you are working with an old machine, use 0.5.x.

[jmwhitha]

That's very helpful! Thank you! Can you tell me where I can get the right package? Does SSE2 have a different name on sourceforge? Does it come in one of these libraries?
libraries:

- libatlas-base-dev
#- libatlas-dev
- libblas-dev
- liblapack-dev
- libeigen3-dev
- libc6-dev
- libzip-dev
- libbz2-dev
- zlib1g-dev
- libcurl4-openssl-dev
- libgsl0-dev
- libgsl0ldbl
- gsl-bin
- mime-support
- libncurses5-dev
- libpcre3-dev
- libpng12-dev
- libreadline-dev
- libssl-dev
- uuid
- uuid-dev
- libxml2
- libxml2-dev
- libxslt1-dev
- libxslt1.1
- xz-utils
- liblzma-dev
- zlib1g-dev

Thank you again and God bless,
Jason

[Richard Finney]

Run this:

cat /proc/cpuinfo | grep flags

Should get output like this ....
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt rdtscp lm 3dnowext 3dnow pni cx16 lahf_lm cmp_legacy svm extapic cr8_legacy
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt rdtscp lm 3dnowext 3dnow pni cx16 lahf_lm cmp_legacy svm extapic cr8_legacy
[ ... more output removed ]

Look for sse2.

If you have it , good. Otherwise use an older version of bwa.

gcc has the -msse2 flag; you might try it.

[jmwhitha]

Thank you! Yes, I see the sse2 in my second set of flags. I also apt-get the gcc, but still when I execute make, I get the same error. What do you suggest?

[Richard Finney]

This might work.

Try the -msse2 flag.

Append to CFLAGS line in "Makefile" ....
like this ...

CFLAGS= -g -Wall -O2 -msse2

[lorendarith]

This might work.

Try the -msse2 flag.

Append to CFLAGS line in "Makefile" ....
like this ...

CFLAGS= -g -Wall -O2 -msse2

I'm in the same boat as OP, but this did not work unfortunately :/

[Richard Finney]

Some clown gave you either a bum gcc or butchered your include file system.
SSE2's been around since 2001 and you DO have it.
You could try downloading and making your own gcc but this is a hassle.

If you have a sysadmin, talk with him. Ask them to update gcc. If you are the sysadmin on your own system, re-install an upgraded gcc.

[lh3]

SSE2 is present on all x86_64, but not all i686 has that. Given that you can find the sse2 flag from /proc/cpuinfo, your system must have that. 4.7 is pretty new. I use 4.2.1. I guess this gcc is compiled without the SSE2 support. If so, you should compile gcc from source.

[jmwhitha]

A whole new set of warnings came up when I changed the make file.

jmwhitha@Linux-OptiPlex-755:~/bwa-0.7.3a$ make
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD ksw.c -o ksw.o
gcc -c -g -Wall -O2 -msse2 -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 -msse2 -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 -msse2 -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 -msse2 -DHAVE_PTHREAD bwamem.c -o bwamem.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o
bwamem_pair.c: In function ‘mem_pestat’:
bwamem_pair.c:59:2: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ [-Wformat]
bwamem_pair.c:59:2: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ [-Wformat]
bwamem_pair.c:59:2: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ [-Wformat]
bwamem_pair.c:59:2: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 7 has type ‘size_t’ [-Wformat]
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 -msse2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o
gcc -c -g -Wall -O2 -msse2 -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 -msse2 -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 -msse2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bamlite.c -o bamlite.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD is.c -o is.o
gcc -c -g -Wall -O2 -msse2 -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 -msse2 -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 -msse2 -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 -msse2 -DHAVE_PTHREAD pemerge.c -o pemerge.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -Wall -O2 -msse2 -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 -msse2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD fastmap.c -o fastmap.o
fastmap.c: In function ‘main_fastmap’:
fastmap.c:164:3: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ [-Wformat]
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o
gcc -c -g -Wall -O2 -msse2 -DHAVE_PTHREAD main.c -o main.o
gcc -g -Wall -O2 -msse2 -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 -msse2 -DHAVE_PTHREAD example.c -o example.o
gcc -g -Wall -O2 -msse2 -DHAVE_PTHREAD example.o -o bwamem-lite -L. -lbwa -lm -lz -lpthread

[Richard Finney]

You're good. I think. Those are just warnings, not errors.

[jmwhitha]

I have SSE2 according to cat /proc/cpuinfo | grep flags, but I do not have msse2. I have i686 and when I execute apt-get install gcc, it says I have the newest version of gcc. When you says, "from the source", are you saying that I wget from ubuntu? What is the command?

[Richard Finney]

Seriously, you're probably good. Ignore the warnings.
What happens when you run bwa ? Just type "./bwa".

Making gcc from source is major hassle and you're gcc is up to date.

[jmwhitha]

Thank you very much Richard! The compiling seems to have worked.

There seems to be a new problem now though with the SAM file only containing header lines and no alignment lines. I am posting a new topic for this.

[jmwhitha]

Here it is:

http://seqanswers.com/forums/showthread.php?p=102650#post102650