BWA installation failure

[Jurek]

Hello World,

I downloaded the bwa version 5.7 and cannot compile it.

[Jurek@fg-pc22 bwa-0.5.7]$ make
make[1]: Entering directory `/home/Jurek/Desktop/bwa2/bwa-0.5.7'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/home/Jurek/Desktop/bwa2/bwa-0.5.7'
make[1]: Entering directory `/home/Jurek/Desktop/bwa2/bwa-0.5.7/bwt_gen'
gcc -c -g -Wall -O2 -m64 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o
bwt_gen.c:1: sorry, unimplemented: 64-bit mode not compiled in
make[1]: *** [bwt_gen.o] Error 1
make[1]: Leaving directory `/home/Jurek/Desktop/bwa2/bwa-0.5.7/bwt_gen'
make: *** [lib-recur] Error 1

What am I doing wrong (I appreciate it may be very simple)?

[lh3]

Remove -m64 from the "CFLAGS" line in Makefile. Nonetheless, bwa works better on 64-bit machines.

[Jurek]

It worked. Thank you!

[chrisW]

similar install problems

Greetings, I am novice as novice can be. I have a rudimentary knowledge of things UNIX, so understanding the error messages is currently difficult. I had a similar error wrt -m64. I removed that from the CFLAGS line and now have different errors. To whit:

Error code 127, which follows immediately after 2 lines that start "gcc" and two lines that appear to be instructing some change to

ar -cru libbwtgen.a bwt_gen.o QSufSort.o

and then the following Stop messages:

Stop in .../bwa-0.5.7/bwt_gen (line 18 of Makefile) Error code 1

Stop in..../bwa-0.5.7 (line 33 of Makefile)

Any help would be much appreciated!

[chrisW]

similar install problems

Greetings, I am novice as novice can be. I have a rudimentary knowledge of things UNIX, so understanding the error messages is currently difficult. I had a similar error wrt -m64. I removed that from the CFLAGS line and now have different errors. To whit:

Error code 127, which follows immediately after 2 lines that start "gcc" and two lines that appear to be instructing some change to

ar -cru libbwtgen.a bwt_gen.o QSufSort.o

and then the following Stop messages:

Stop in .../bwa-0.5.7/bwt_gen (line 18 of Makefile) Error code 1

Stop in..../bwa-0.5.7 (line 33 of Makefile)

Any help would be much appreciated!

[raela]

It would be more helpful if you could produce the full results of 'make'. You can use code tags to keep the paste to a reasonable size. Try [code]make results here.[/code]

[chrisW]

I should note that I'm using a Windows 7 machine. I have downloaded the Subsystem for Unix-based apps and have been teaching myself the basic use of Korn Shell. When I type "make" into the ksh prompt the following appears:

ar -cru libbwtgen.a bwt_gen.o QSufSort.o
ar: Either the AR_LIBRARIAN environment variable must be set
ar: or you must include the directory containing 'lib.exe' in PATH
***Error code 127

Stop in /dev/fs/C/Users/my.name/Desktop/Mastigo-genomics/bwa-0.5.7/bwt_gen (line 18 of Makefile).
***Error Code 1

Stop in /dev/fs/C/Users/my.name/Desktop/Mastigo-genomics/bwa-0.5.7 (line 33 of Makefile).

[drio]

I should note that I'm using a Windows 7 machine. I have downloaded the Subsystem for Unix-based apps and have been teaching myself the basic use of Korn Shell. When I type "make" into the ksh prompt the following appears:

ar -cru libbwtgen.a bwt_gen.o QSufSort.o
ar: Either the AR_LIBRARIAN environment variable must be set
ar: or you must include the directory containing 'lib.exe' in PATH
***Error code 127

Stop in /dev/fs/C/Users/my.name/Desktop/Mastigo-genomics/bwa-0.5.7/bwt_gen (line 18 of Makefile).
***Error Code 1

Stop in /dev/fs/C/Users/my.name/Desktop/Mastigo-genomics/bwa-0.5.7 (line 33 of Makefile).

Are you using cygwin?

If not install it: http://www.cygwin.com/

It will install the POSIX libraries and the environment to compile bwa and other open sources tools.

[t59175]

not enough memory allocated

Hello,

I am using bwa-0.5.8c and I got an installation failure Error 1. After successful compilation without -m4 in the CFLAGS line, I got an error message saying not enough memory allocated when running it. I have 136G memory. I'd like to know how to allocate more memory. Thanks,

[t59175]

If the 32bit installation restricted memmory usage to about 3GB. Then Can onyone tell me how to install it on ia64 machine? Thanks.

[fenciso]

Hello,

I am new using bwa. I am trying to install bwa-0.5.9 but I can not compile it:

make[1]: Entering directory `/local/home/felix/cornell/bwa-0.5.9'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/local/home/felix/cornell/bwa-0.5.9'
make[1]: Entering directory `/local/home/felix/cornell/bwa-0.5.9/bwt_gen'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/local/home/felix/cornell/bwa-0.5.9/bwt_gen'
gcc -g -Wall -O2 -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 bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
utils.o: In function `err_xzopen_core':
/local/home/felix/cornell/bwa-0.5.9/utils.c:61: undefined reference to `egzopen'
/local/home/felix/cornell/bwa-0.5.9/utils.c:60: undefined reference to `egzdopen'
bntseq.o: In function `ks_getuntil':
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:37: undefined reference to `egzread'
bntseq.o: In function `ks_getc':
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:191: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:37: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:237: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:237: undefined reference to `egzread'
bntseq.o: In function `bwa_fa2pac':
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:265: undefined reference to `egzclose'
bwtindex.o: In function `bwa_index':
/local/home/felix/cornell/bwa-0.5.9/bwtindex.c:84: undefined reference to `egzclose'
/local/home/felix/cornell/bwa-0.5.9/bwtindex.c:92: undefined reference to `egzclose'
simple_dp.o: In function `ks_getuntil':
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:11: undefined reference to `egzread'
simple_dp.o: In function `ks_getc':
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
simple_dp.o: In function `load_seqs':
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:83: undefined reference to `egzclose'
simple_dp.o: In function `aln_seqs':
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:126: undefined reference to `egzclose'
bwaseqio.o: In function `ks_getuntil':
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:8: undefined reference to `egzread'
bwaseqio.o: In function `bwa_seq_close':
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:49: undefined reference to `egzclose'
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:47: undefined reference to `egzclose'
bwaseqio.o: In function `bwa_bam_open':
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:28: undefined reference to `egzopen'
bwaseqio.o: In function `ks_getc':
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:105: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:8: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:177: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:177: undefined reference to `egzread'
bwtsw2_aux.o: In function `ks_getuntil':
/local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:18: undefined reference to `egzread'
bwtsw2_aux.o:/local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:624: more undefined references to `egzread' follow
bwtsw2_aux.o: In function `bsw2_aln':
/local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:648: undefined reference to `egzclose'
bamlite.o: In function `bam_read1':
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:131: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:135: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:151: undefined reference to `egzread'
bamlite.o: In function `bam_header_read':
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:80: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:87: undefined reference to `egzread'
bamlite.o:/local/home/felix/cornell/bwa-0.5.9/bamlite.c:90: more undefined references to `egzread' follow
collect2: ld returned 1 exit status
make: *** [bwa] Error 1

I do not what is the problem

[nilshomer]

The answer is found in this forum (try searching first):

http://seqanswers.com/forums/showthread.php?t=6155

[l.miozzi]

Hi,
I have the same problem. When I type "make", I obtained this error:
/home/lauram/bin/bwa-0.5.9/bwtsw2_aux.c:635: undefined reference to `egzread'
bamlite.o: In function `bam_read1':
/home/lauram/bin/bwa-0.5.9/bamlite.c:131: undefined reference to `egzread'
bamlite.o:/home/lauram/bin/bwa-0.5.9/bamlite.c:135: more undefined references to `egzread' follow
collect2: ld returned 1 exit status
make: *** [bwa] Error 1


Does anyone can help, please?

Thanks!

Hello,

I am new using bwa. I am trying to install bwa-0.5.9 but I can not compile it:

make[1]: Entering directory `/local/home/felix/cornell/bwa-0.5.9'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/local/home/felix/cornell/bwa-0.5.9'
make[1]: Entering directory `/local/home/felix/cornell/bwa-0.5.9/bwt_gen'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/local/home/felix/cornell/bwa-0.5.9/bwt_gen'
gcc -g -Wall -O2 -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 bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
utils.o: In function `err_xzopen_core':
/local/home/felix/cornell/bwa-0.5.9/utils.c:61: undefined reference to `egzopen'
/local/home/felix/cornell/bwa-0.5.9/utils.c:60: undefined reference to `egzdopen'
bntseq.o: In function `ks_getuntil':
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:37: undefined reference to `egzread'
bntseq.o: In function `ks_getc':
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:191: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:37: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:237: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:237: undefined reference to `egzread'
bntseq.o: In function `bwa_fa2pac':
/local/home/felix/cornell/bwa-0.5.9/bntseq.c:265: undefined reference to `egzclose'
bwtindex.o: In function `bwa_index':
/local/home/felix/cornell/bwa-0.5.9/bwtindex.c:84: undefined reference to `egzclose'
/local/home/felix/cornell/bwa-0.5.9/bwtindex.c:92: undefined reference to `egzclose'
simple_dp.o: In function `ks_getuntil':
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:11: undefined reference to `egzread'
simple_dp.o: In function `ks_getc':
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:130: undefined reference to `egzread'
simple_dp.o: In function `load_seqs':
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:83: undefined reference to `egzclose'
simple_dp.o: In function `aln_seqs':
/local/home/felix/cornell/bwa-0.5.9/simple_dp.c:126: undefined reference to `egzclose'
bwaseqio.o: In function `ks_getuntil':
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:8: undefined reference to `egzread'
bwaseqio.o: In function `bwa_seq_close':
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:49: undefined reference to `egzclose'
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:47: undefined reference to `egzclose'
bwaseqio.o: In function `bwa_bam_open':
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:28: undefined reference to `egzopen'
bwaseqio.o: In function `ks_getc':
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:105: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:8: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:177: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bwaseqio.c:177: undefined reference to `egzread'
bwtsw2_aux.o: In function `ks_getuntil':
/local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:18: undefined reference to `egzread'
bwtsw2_aux.o:/local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:624: more undefined references to `egzread' follow
bwtsw2_aux.o: In function `bsw2_aln':
/local/home/felix/cornell/bwa-0.5.9/bwtsw2_aux.c:648: undefined reference to `egzclose'
bamlite.o: In function `bam_read1':
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:131: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:135: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:151: undefined reference to `egzread'
bamlite.o: In function `bam_header_read':
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:80: undefined reference to `egzread'
/local/home/felix/cornell/bwa-0.5.9/bamlite.c:87: undefined reference to `egzread'
bamlite.o:/local/home/felix/cornell/bwa-0.5.9/bamlite.c:90: more undefined references to `egzread' follow
collect2: ld returned 1 exit status
make: *** [bwa] Error 1

I do not what is the problem

[nilshomer]

Did you follow the link or attempt at all to search for it? You can imagine our frustration when the post above gives a link to the answer?

[l.miozzi]

I tried to follow the link but it didn't work, so I decided to post my problem.
Thanks to one of my colleagues I find out what was the problem...the ubuntu release in the server wasn't updated...so now everything is working.

Thanks

Laura