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Old 01-18-2016, 06:49 AM   #1
carolW
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Location: US

Join Date: Apr 2013
Posts: 103
Default tmap aligner

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
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Old 01-18-2016, 06:52 AM   #2
skbrimer
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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
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Old 01-18-2016, 06:56 AM   #3
carolW
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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?
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Old 01-18-2016, 07:02 AM   #4
skbrimer
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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.
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Old 01-18-2016, 07:10 AM   #5
skbrimer
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Quote:
Originally Posted by carolW View Post
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
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Old 01-18-2016, 07:40 AM   #6
carolW
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Location: US

Join Date: Apr 2013
Posts: 103
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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

Quote:
Originally Posted by skbrimer View Post
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.
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Old 01-18-2016, 07:43 AM   #7
skbrimer
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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?
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Old 01-18-2016, 07:47 AM   #8
Richard Finney
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You are missing bzip2 development library. Bzip2 is , I believe, separate from boost (shudder).

Try this ...

sudo apt-get install libbz2-dev
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Old 01-18-2016, 07:51 AM   #9
carolW
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it works now. I took all commands from github.

Many thx
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Old 01-19-2016, 02:29 AM   #10
carolW
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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...
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Old 01-19-2016, 06:35 AM   #11
skbrimer
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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.
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Old 01-19-2016, 06:43 AM   #12
carolW
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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
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Old 01-19-2016, 06:46 AM   #13
GenoMax
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How much memory do you have on this machine @carolW?
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Old 01-19-2016, 06:51 AM   #14
skbrimer
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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
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Old 01-19-2016, 06:58 AM   #15
GenoMax
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@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.
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Old 01-19-2016, 07:50 AM   #16
carolW
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15G. but I had expected that if there is no enough mem, a msg will be displayed. when I ran without all params like tmap index -f ~/ucscHg19/hg19.fa, no file was created and no msg was displayed. will run it on a machine with a larger RAM

Thanks
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Old 01-19-2016, 09:31 AM   #17
skbrimer
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Hi carolW, I am not sure how to help you anymore, you have run out of my experience but I do have a few suggestions.

1.) if you have acess (you or someone) to the torrent server hg19 is already installed under /results/analysis/output/tmap-f3/hg19 and you could just copy those files to your machine.

2.) try it on a larger machine

3.) try asking for advice on the torrent community or the github repo both are monitored by the developers so they should be able to help you.

Again, I'm sorry I could not be more helpful, I just have never ran into that problem.
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