[musohail]

Hello Colleagues

I have installed BWA-0.7.17 many times. It works fine. It has all the commands in it. It does well with BWA index.
But it doesnt work for bwa mem. saying mem is not a command.
Whe I type only bwa. it gives all other command options except mem.
On my other computer it also have mem command but I do not use that computer. Please help

Usage: bwa <command> [options]

Command: index index sequences in the FASTA format
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries
fastmap identify super-maximal exact matches

fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
bwt2sa generate SA from BWT and Occ
pac2cspac convert PAC to color-space PAC
stdsw standard SW/NW alignment

[Sidrah]

Hi,

I am new in the bio.
I need to install the BWA on my window but have problem by zlib
I have already downloaded the last version of BWA and the zlib and I use the Visual Studio 2017 for compiling.
I do not know how to run.
F:\BIO\bwa>make all
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
utils.c:33:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
compilation terminated.
make: *** [utils.o] Error 1


Would you please help me?

Did you find the solution to this problem for windows?? I m also having the same problem.

[Fahim123]

Hi,

I am new in the bio.
I need to install the BWA on my window but have problem by zlib
I have already downloaded the last version of BWA and the zlib and I use the Visual Studio 2017 for compiling.
I do not know how to run.
F:\BIO\bwa>make all
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
utils.c:33:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^
compilation terminated.
make: *** [utils.o] Error 1


Would you please help me?

[nilshomer]

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

Just tried the link, it links to seqanswers.com, so... I am glad you solved the problem.

[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

[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]

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]

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

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

[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

[t59175]

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

[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,

[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.

[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).

[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]

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!