tmap aligner

[carolW]

Hi,
I tried to install TMAP but got the following error when invoking make

src/util/../seq/../io/tmap_file.h:6:18: fatal error: zlib.h: No such file or directory
#include <zlib.h>

the zlib.h file is not in src/util. is there a bug and what to do to solve the problem?

Thanks

Carol

[skbrimer]

Hi Carol,
There is not a bug and you are missing an external library dependency "zlib1g-dev" if you install that library and redo the build script it should work just fine.
Sean

[carolW]

I installed this library but got another error

src/util/../seq/../io/tmap_file.h:8:19: fatal error: bzlib.h: No such file or directory
#include <bzlib.h>

which library should be installed for this?

[skbrimer]

Okay, I'm going to assume you are using Ubuntu for this so cut and paste the following in your terminal window.

apt-get update

apt-get install \
build-essential \
git-core \
cmake \
liblapack-dev \
liblapack3gf \
libblas-dev \
libblas3gf \
libatlas-base-dev \
gfortran \
zlib1g-dev \
libgsl0-dev \
libbz2-dev \
libcurl4-openssl-dev \
libncurses5-dev \
libboost-serialization-dev \
libhdf5-dev \
r-base


This is taken form the BUILD.txt file, it tells you everything you need to install.

[skbrimer]

I installed this library but got another error

src/util/../seq/../io/tmap_file.h:8:19: fatal error: bzlib.h: No such file or directory
#include <bzlib.h>

which library should be installed for this?

sorry I didn't answer this question as well. The library you are wanting is the boost library. Its in the list for the BUILD file.

Good Luck

[carolW]

Where is the build file located (apologies for my ignorance)?

I installed all the suggested packages but got some warnings and errors that I enclose below.

gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bam_plcmd.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bam_plcmd.o src/samtools/bam_plcmd.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/sam_view.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/sam_view.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/sam_view.o src/samtools/sam_view.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bam_rmdup.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bam_rmdup.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bam_rmdup.o src/samtools/bam_rmdup.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bam_rmdupse.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bam_rmdupse.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bam_rmdupse.o src/samtools/bam_rmdupse.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bam_mate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bam_mate.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bam_mate.o src/samtools/bam_mate.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bam_stat.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bam_stat.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bam_stat.o src/samtools/bam_stat.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bam_color.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bam_color.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bam_color.o src/samtools/bam_color.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bam2bcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bam2bcf.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bam2bcf.o src/samtools/bam2bcf.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bam2bcf_indel.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bam2bcf_indel.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bam2bcf_indel.o src/samtools/bam2bcf_indel.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/errmod.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/errmod.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/errmod.o src/samtools/errmod.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/sample.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/sample.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/sample.o src/samtools/sample.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/cut_target.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/cut_target.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/cut_target.o src/samtools/cut_target.c &&\
mv -f $depbase.Tpo $depbase.Po
src/samtools/cut_target.c: In function ‘main_cut_target’:
src/samtools/cut_target.c:137:36: warning: variable ‘lastpos’ set but not used [-Wunused-but-set-variable]
int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
^
depbase=`echo src/samtools/phase.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/phase.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/phase.o src/samtools/phase.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bam2depth.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bam2depth.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bam2depth.o src/samtools/bam2depth.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/padding.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/padding.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/padding.o src/samtools/padding.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/bcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/bcf.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/bcf.o src/samtools/bcftools/bcf.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/bcf2qcall.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/bcf2qcall.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/bcf2qcall.o src/samtools/bcftools/bcf2qcall.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/bcfutils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/bcfutils.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/bcfutils.o src/samtools/bcftools/bcfutils.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/call1.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/call1.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/call1.o src/samtools/bcftools/call1.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/em.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/em.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/em.o src/samtools/bcftools/em.c &&\
mv -f $depbase.Tpo $depbase.Po
src/samtools/bcftools/em.c: In function ‘bcf_em1’:
src/samtools/bcftools/em.c:174:12: warning: variable ‘n2’ set but not used [-Wunused-but-set-variable]
int i, n, n2;
^
depbase=`echo src/samtools/bcftools/fet.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/fet.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/fet.o src/samtools/bcftools/fet.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/index.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/index.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/index.o src/samtools/bcftools/index.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/kfunc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/kfunc.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/kfunc.o src/samtools/bcftools/kfunc.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/kmin.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/kmin.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/kmin.o src/samtools/bcftools/kmin.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/main.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/main.o src/samtools/bcftools/main.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/mut.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/mut.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/mut.o src/samtools/bcftools/mut.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/prob1.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/prob1.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/prob1.o src/samtools/bcftools/prob1.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bcftools/vcf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bcftools/vcf.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bcftools/vcf.o src/samtools/bcftools/vcf.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/samtools/bamtk.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/samtools/bamtk.o -MD -MP -MF $depbase.Tpo -c -o src/samtools/bamtk.o src/samtools/bamtk.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/server/tmap_server.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/server/tmap_server.o -MD -MP -MF $depbase.Tpo -c -o src/server/tmap_server.o src/server/tmap_server.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/server/tmap_shm.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/server/tmap_shm.o -MD -MP -MF $depbase.Tpo -c -o src/server/tmap_shm.o src/server/tmap_shm.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/sam2fs/tmap_sam2fs_aux.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/sam2fs/tmap_sam2fs_aux.o -MD -MP -MF $depbase.Tpo -c -o src/sam2fs/tmap_sam2fs_aux.o src/sam2fs/tmap_sam2fs_aux.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/sam2fs/tmap_sam2fs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/sam2fs/tmap_sam2fs.o -MD -MP -MF $depbase.Tpo -c -o src/sam2fs/tmap_sam2fs.o src/sam2fs/tmap_sam2fs.c &&\
mv -f $depbase.Tpo $depbase.Po
src/sam2fs/tmap_sam2fs.c: In function ‘tmap_sam2fs_aux’:
src/sam2fs/tmap_sam2fs.c:368:31: warning: variable ‘read_bases_mem’ set but not used [-Wunused-but-set-variable]
int32_t read_bases_len = 0, read_bases_mem = 256;
^
depbase=`echo src/index/tmap_index_speed.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/index/tmap_index_speed.o -MD -MP -MF $depbase.Tpo -c -o src/index/tmap_index_speed.o src/index/tmap_index_speed.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/index/tmap_bwt_check.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/index/tmap_bwt_check.o -MD -MP -MF $depbase.Tpo -c -o src/index/tmap_bwt_check.o src/index/tmap_bwt_check.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/index/tmap_bwt_compare.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/index/tmap_bwt_compare.o -MD -MP -MF $depbase.Tpo -c -o src/index/tmap_bwt_compare.o src/index/tmap_bwt_compare.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/util/tmap_map_opt.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/util/tmap_map_opt.o -MD -MP -MF $depbase.Tpo -c -o src/map/util/tmap_map_opt.o src/map/util/tmap_map_opt.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/util/tmap_map_stats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/util/tmap_map_stats.o -MD -MP -MF $depbase.Tpo -c -o src/map/util/tmap_map_stats.o src/map/util/tmap_map_stats.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/util/tmap_map_util.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/util/tmap_map_util.o -MD -MP -MF $depbase.Tpo -c -o src/map/util/tmap_map_util.o src/map/util/tmap_map_util.c &&\
mv -f $depbase.Tpo $depbase.Po
src/map/util/tmap_map_util.c: In function ‘tmap_map_util_mapq’:
src/map/util/tmap_map_util.c:841:11: warning: variable ‘stage’ set but not used [-Wunused-but-set-variable]
int32_t stage = -1;
^
src/map/util/tmap_map_util.c:837:14: warning: variable ‘best_i’ set but not used [-Wunused-but-set-variable]
int32_t i, best_i;
^
src/map/util/tmap_map_util.c: In function ‘tmap_map_util_sw_gen_score_helper’:
src/map/util/tmap_map_util.c:1105:38: warning: variable ‘end_pos_prev’ set but not used [-Wunused-but-set-variable]
uint32_t start_pos_prev=0, end_pos_prev=0;
^
src/map/util/tmap_map_util.c: In function ‘tmap_map_util_sw_gen_score’:
src/map/util/tmap_map_util.c:1275:12: warning: variable ‘start_pos_prev’ set but not used [-Wunused-but-set-variable]
uint32_t start_pos_prev=0, end_pos_prev=0;
^
src/map/util/tmap_map_util.c: In function ‘tmap_map_util_fsw’:
src/map/util/tmap_map_util.c:2762:11: warning: variable ‘start_softclip_len’ set but not used [-Wunused-but-set-variable]
int32_t start_softclip_len = 0;
^
depbase=`echo src/map/pairing/tmap_map_pairing.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/pairing/tmap_map_pairing.o -MD -MP -MF $depbase.Tpo -c -o src/map/pairing/tmap_map_pairing.o src/map/pairing/tmap_map_pairing.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map1/tmap_map1.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map1/tmap_map1.o -MD -MP -MF $depbase.Tpo -c -o src/map/map1/tmap_map1.o src/map/map1/tmap_map1.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map1/tmap_map1_aux.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map1/tmap_map1_aux.o -MD -MP -MF $depbase.Tpo -c -o src/map/map1/tmap_map1_aux.o src/map/map1/tmap_map1_aux.c &&\
mv -f $depbase.Tpo $depbase.Po
src/map/map1/tmap_map1_aux.c: In function ‘tmap_map1_aux_core’:
src/map/map1/tmap_map1_aux.c:668:36: warning: variable ‘cigar_i’ set but not used [-Wunused-but-set-variable]
uint32_t op, op_len, cigar_i;
^
depbase=`echo src/map/map2/tmap_map2.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map2/tmap_map2.o -MD -MP -MF $depbase.Tpo -c -o src/map/map2/tmap_map2.o src/map/map2/tmap_map2.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map2/tmap_map2_aux.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map2/tmap_map2_aux.o -MD -MP -MF $depbase.Tpo -c -o src/map/map2/tmap_map2_aux.o src/map/map2/tmap_map2_aux.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map2/tmap_map2_chain.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map2/tmap_map2_chain.o -MD -MP -MF $depbase.Tpo -c -o src/map/map2/tmap_map2_chain.o src/map/map2/tmap_map2_chain.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map2/tmap_map2_core.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map2/tmap_map2_core.o -MD -MP -MF $depbase.Tpo -c -o src/map/map2/tmap_map2_core.o src/map/map2/tmap_map2_core.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map2/tmap_map2_mempool.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map2/tmap_map2_mempool.o -MD -MP -MF $depbase.Tpo -c -o src/map/map2/tmap_map2_mempool.o src/map/map2/tmap_map2_mempool.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map3/tmap_map3.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map3/tmap_map3.o -MD -MP -MF $depbase.Tpo -c -o src/map/map3/tmap_map3.o src/map/map3/tmap_map3.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map3/tmap_map3_aux.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map3/tmap_map3_aux.o -MD -MP -MF $depbase.Tpo -c -o src/map/map3/tmap_map3_aux.o src/map/map3/tmap_map3_aux.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map4/tmap_map4.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map4/tmap_map4.o -MD -MP -MF $depbase.Tpo -c -o src/map/map4/tmap_map4.o src/map/map4/tmap_map4.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/map4/tmap_map4_aux.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/map4/tmap_map4_aux.o -MD -MP -MF $depbase.Tpo -c -o src/map/map4/tmap_map4_aux.o src/map/map4/tmap_map4_aux.c &&\
mv -f $depbase.Tpo $depbase.Po
src/map/map4/tmap_map4_aux.c: In function ‘tmap_map4_aux_core’:
src/map/map4/tmap_map4_aux.c:255:32: warning: variable ‘qend’ set but not used [-Wunused-but-set-variable]
uint32_t qstart, qend;
^
src/map/map4/tmap_map4_aux.c:252:30: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
tmap_bwt_int_t tmp;
^
depbase=`echo src/map/mapvsw/tmap_map_vsw.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/mapvsw/tmap_map_vsw.o -MD -MP -MF $depbase.Tpo -c -o src/map/mapvsw/tmap_map_vsw.o src/map/mapvsw/tmap_map_vsw.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/mapall/tmap_map_all.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/mapall/tmap_map_all.o -MD -MP -MF $depbase.Tpo -c -o src/map/mapall/tmap_map_all.o src/map/mapall/tmap_map_all.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/map/tmap_map_driver.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/map/tmap_map_driver.o -MD -MP -MF $depbase.Tpo -c -o src/map/tmap_map_driver.o src/map/tmap_map_driver.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/tmap_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -Wall -g -O3 -pthread -msse3 -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -MT src/tmap_main.o -MD -MP -MF $depbase.Tpo -c -o src/tmap_main.o src/tmap_main.c &&\
mv -f $depbase.Tpo $depbase.Po
g++ -Wall -g -O3 -pthread -msse3 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -Isrc/samtools -o tmap src/util/tmap_alloc.o src/util/tmap_definitions.o src/util/tmap_error.o src/util/tmap_rand.o src/util/tmap_time.o src/util/tmap_fibheap.o src/util/tmap_progress.o src/util/tmap_string.o src/util/tmap_levenshtein.o src/util/tmap_sam_convert.o src/seq/tmap_fq.o src/seq/tmap_sff.o src/seq/tmap_sam.o src/seq/tmap_seq.o src/seq/tmap_seqs.o src/io/tmap_file.o src/io/tmap_fq_io.o src/io/tmap_sff_io.o src/io/tmap_sam_io.o src/io/tmap_seq_io.o src/io/tmap_seqs_io.o src/index/tmap_bwt.o src/index/tmap_bwt_aux.o src/index/tmap_bwtl.o src/index/tmap_bwt_gen.o src/index/tmap_bwt_match.o src/index/tmap_bwt_match_hash.o src/index/tmap_bwt_smem.o src/index/tmap_index.o src/index/tmap_refseq.o src/index/tmap_sa.o src/index/tmap_sa_aux.o src/index/tmap_index_size.o src/sw/tmap_sw.o src/sw/tmap_fsw.o src/sw/tmap_vsw_definitions.o src/sw/tmap_vsw.o src/sw/lib/vsw.o src/sw/lib/vsw16.o src/sw/lib/sw-vector.o src/sw/lib/Solution.o src/sw/lib/Solution1.o src/sw/lib/Solution2.o src/sw/lib/Solution3.o src/sw/lib/Solution4.o src/sw/lib/Solution5.o src/sw/lib/Solution6.o src/sw/lib/Solution7.o src/sw/lib/Solution8.o src/sw/lib/Solution9.o src/sw/lib/Solution10.o src/sw/lib/AffineSWOptimization.o src/sw/lib/AffineSWOptimizationHash.o src/sw/lib/AffineSWOptimizationWrapper.o src/sw/tmap_vsw_bm.o src/samtools/bam.o src/samtools/sam.o src/samtools/sam_header.o src/samtools/bam_import.o src/samtools/bam_aux.o src/samtools/bam_pileup.o src/samtools/bam_lpileup.o src/samtools/bam_md.o src/samtools/faidx.o src/samtools/bedidx.o src/samtools/razf.o src/samtools/bgzf.o src/samtools/kstring.o src/samtools/knetfile.o src/samtools/kaln.o src/samtools/kprobaln.o src/samtools/bam_index.o src/samtools/bam_sort.o src/samtools/bam_reheader.o src/samtools/bam_cat.o src/samtools/bam_tview.o src/samtools/bam_plcmd.o src/samtools/sam_view.o src/samtools/bam_rmdup.o src/samtools/bam_rmdupse.o src/samtools/bam_mate.o src/samtools/bam_stat.o src/samtools/bam_color.o src/samtools/bam2bcf.o src/samtools/bam2bcf_indel.o src/samtools/errmod.o src/samtools/sample.o src/samtools/cut_target.o src/samtools/phase.o src/samtools/bam2depth.o src/samtools/padding.o src/samtools/bcftools/bcf.o src/samtools/bcftools/bcf2qcall.o src/samtools/bcftools/bcfutils.o src/samtools/bcftools/call1.o src/samtools/bcftools/em.o src/samtools/bcftools/fet.o src/samtools/bcftools/index.o src/samtools/bcftools/kfunc.o src/samtools/bcftools/kmin.o src/samtools/bcftools/main.o src/samtools/bcftools/mut.o src/samtools/bcftools/prob1.o src/samtools/bcftools/vcf.o src/samtools/bamtk.o src/server/tmap_server.o src/server/tmap_shm.o src/sam2fs/tmap_sam2fs_aux.o src/sam2fs/tmap_sam2fs.o src/index/tmap_index_speed.o src/index/tmap_bwt_check.o src/index/tmap_bwt_compare.o src/map/util/tmap_map_opt.o src/map/util/tmap_map_stats.o src/map/util/tmap_map_util.o src/map/pairing/tmap_map_pairing.o src/map/map1/tmap_map1.o src/map/map1/tmap_map1_aux.o src/map/map2/tmap_map2.o src/map/map2/tmap_map2_aux.o src/map/map2/tmap_map2_chain.o src/map/map2/tmap_map2_core.o src/map/map2/tmap_map2_mempool.o src/map/map3/tmap_map3.o src/map/map3/tmap_map3_aux.o src/map/map4/tmap_map4.o src/map/map4/tmap_map4_aux.o src/map/mapvsw/tmap_map_vsw.o src/map/mapall/tmap_map_all.o src/map/tmap_map_driver.o src/tmap_main.o -lpthread -lm -lz
src/io/tmap_file.o: In function `tmap_file_fopen':
/home/tmap/TMAP/src/io/tmap_file.c:55: undefined reference to `BZ2_bzReadOpen'
/home/tmap/TMAP/src/io/tmap_file.c:66: undefined reference to `BZ2_bzWriteOpen'
src/io/tmap_file.o: In function `tmap_file_fdopen':
/home/tmap/TMAP/src/io/tmap_file.c:126: undefined reference to `BZ2_bzReadOpen'
/home/tmap/TMAP/src/io/tmap_file.c:137: undefined reference to `BZ2_bzWriteOpen'
src/io/tmap_file.o: In function `tmap_file_fclose1':
/home/tmap/TMAP/src/io/tmap_file.c:176: undefined reference to `BZ2_bzWriteClose'
/home/tmap/TMAP/src/io/tmap_file.c:176: undefined reference to `BZ2_bzWriteClose'
src/io/tmap_file.o: In function `tmap_file_fread':
/home/tmap/TMAP/src/io/tmap_file.c:244: undefined reference to `BZ2_bzRead'
/home/tmap/TMAP/src/io/tmap_file.c:250: undefined reference to `BZ2_bzReadGetUnused'
/home/tmap/TMAP/src/io/tmap_file.c:257: undefined reference to `BZ2_bzReadClose'
/home/tmap/TMAP/src/io/tmap_file.c:265: undefined reference to `BZ2_bzReadOpen'
/home/tmap/TMAP/src/io/tmap_file.c:244: undefined reference to `BZ2_bzRead'
/home/tmap/TMAP/src/io/tmap_file.c:250: undefined reference to `BZ2_bzReadGetUnused'
/home/tmap/TMAP/src/io/tmap_file.c:257: undefined reference to `BZ2_bzReadClose'
/home/tmap/TMAP/src/io/tmap_file.c:265: undefined reference to `BZ2_bzReadOpen'
/home/tmap/TMAP/src/io/tmap_file.c:244: undefined reference to `BZ2_bzRead'
/home/tmap/TMAP/src/io/tmap_file.c:250: undefined reference to `BZ2_bzReadGetUnused'
/home/tmap/TMAP/src/io/tmap_file.c:257: undefined reference to `BZ2_bzReadClose'
/home/tmap/TMAP/src/io/tmap_file.c:265: undefined reference to `BZ2_bzReadOpen'
src/io/tmap_file.o: In function `tmap_file_fwrite':
/home/tmap/TMAP/src/io/tmap_file.c:340: undefined reference to `BZ2_bzwrite'
collect2: error: ld returned 1 exit status
make[2]: *** [tmap] Error 1
make[2]: Leaving directory `/home/tmap/TMAP'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/tmap/TMAP'
make: *** [all] Error 2

Okay, I'm going to assume you are using Ubuntu for this so cut and paste the following in your terminal window.

apt-get update

apt-get install \
build-essential \
git-core \
cmake \
liblapack-dev \
liblapack3gf \
libblas-dev \
libblas3gf \
libatlas-base-dev \
gfortran \
zlib1g-dev \
libgsl0-dev \
libbz2-dev \
libcurl4-openssl-dev \
libncurses5-dev \
libboost-serialization-dev \
libhdf5-dev \
r-base


This is taken form the BUILD.txt file, it tells you everything you need to install.

[skbrimer]

no problems, I think I see what you are doing wrong because it is what I did wrong, Did you go to github and clone(download) only the TMAP subdirectory?

[Richard Finney]

You are missing bzip2 development library. Bzip2 is , I believe, separate from boost (shudder).

Try this ...

sudo apt-get install libbz2-dev

[carolW]

it works now. I took all commands from github.

Many thx

[carolW]

I tried to index the hg19 but it seems to stuck. What's wrong or which other params should be used?

tmap index -a bwtsw -f ~/ucscHg19/hg19.fa

src/index/tmap_refseq.c:228: in function "tmap_refseq_fasta2pac"
IUPAC codes were found and will be converted to non-matching DNA bases
warning: the value is out of range
trying to continue...

[skbrimer]

you should be fine, its just saying it found an ambigous base pair and is fixing it. If you look in the folder with your referance if it worked, there should be a ".tmap.anno", "tmap.bwt", .tmap.pac", and a "tmap.sa" file when you are done.

The fasta index will have to be done using samtools faidx command, tmap does not compile that one.

[carolW]

No file was created. In another run, I ran

tmap index -a bwtsw -f ~/ucscHg19/hg19.fa -o 32 -i 1 -H

and got

src/util/tmap_alloc.c:45: in function "tmap_sa_bwt2sa"
sa->sa
fatal error: could not allocate memory

No file was created, either

[GenoMax]

How much memory do you have on this machine @carolW?

[skbrimer]

I'm not sure about human work since I do microbiology, but I thnk @GenoMax may be on the right track. I know that tmap can make the index, here is the techinacl note from Ion http://mendel.iontorrent.com/ion-doc...t_9012907.html

also have you just try running the index without any user overrides? just ;

tmap index -f ~/ucscHg19/hg19.fa

[GenoMax]

@carolW: Before using the human genome try something small (a bacterial genome) to build an index and confirm that everything is installed correctly. My hunch is you don't have enough RAM (document linked by @skbrimer mentions 32GB) or something is not installed right.