Chrysalis Installation appears to have FAILED--Please help

[Chen Dong]

[arcadeo@pw25-32allxbi myBins]$ cd trinityrnaseq-Trinity-v2.5.1/
[arcadeo@pw25-32allxbi trinityrnaseq-Trinity-v2.5.1]$ make
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
                && sh ./configure --prefix=`pwd`  && make install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[1]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm'
Making install in src
make[2]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm/src'
make[3]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm/src'
test -z "/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm/bin" || /bin/mkdir -p "/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm/bin"
  /usr/bin/install -c inchworm cigar_tweaker pull_reads_with_kmers FastaToDeBruijn fastaToKmerCoverageStats '/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm/bin'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm/src'
make[2]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm/src'
make[2]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm'
make[3]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm'
make[2]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm'
make[1]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Inchworm'
cd Chrysalis && make UNSUPPORTED=yes
./MakeDepend: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./MakeDepend)
make[1]: *** [depend] Error 1
make[1]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Chrysalis'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/Chrysalis'
cd trinity-plugins && make trinity_essentials
make[1]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins'
tar xvf seqtk-trinity.v0.0.2.tar.gz
seqtk-trinity-0.0.2/
seqtk-trinity-0.0.2/.gitignore
seqtk-trinity-0.0.2/LICENSE
seqtk-trinity-0.0.2/Makefile
seqtk-trinity-0.0.2/README.md
seqtk-trinity-0.0.2/khash.h
seqtk-trinity-0.0.2/kseq.h
seqtk-trinity-0.0.2/seqtk.c
seqtk-trinity-0.0.2/testing/
seqtk-trinity-0.0.2/testing/newformat_1.fq
seqtk-trinity-0.0.2/testing/newformat_2.fq
seqtk-trinity-0.0.2/testing/oldformat_1.fq
seqtk-trinity-0.0.2/testing/oldformat_2.fq
cd seqtk-trinity-0.0.2 && make
make[2]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/seqtk-trinity-0.0.2'
gcc -g -Wall -O2 -Wno-unused-function seqtk.c -o seqtk-trinity -lz -lm
seqtk.c: In function ‘stk_comp’:
seqtk.c:444:16: warning: variable ‘lc’ set but not used [-Wunused-but-set-variable]
    int la, lb, lc, na, nb, nc, cnt[11];
                ^
make[2]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/seqtk-trinity-0.0.2'
mv seqtk-trinity-0.0.2/seqtk-trinity ./BIN/.
tar -zxvf "ParaFly-0.1.0".tar.gz && \
    cd "ParaFly-0.1.0" && sh ./configure --prefix=`pwd` && make install && \
    cp bin/ParaFly ../BIN/
ParaFly-0.1.0/
ParaFly-0.1.0/LICENSE
ParaFly-0.1.0/Makefile
ParaFly-0.1.0/Makefile.am
ParaFly-0.1.0/Makefile.in
ParaFly-0.1.0/README.md
ParaFly-0.1.0/aclocal.m4
ParaFly-0.1.0/bin/
ParaFly-0.1.0/bin/ParaFly
ParaFly-0.1.0/config.h
ParaFly-0.1.0/config.h.in
ParaFly-0.1.0/config.log
ParaFly-0.1.0/config.status
ParaFly-0.1.0/configure
ParaFly-0.1.0/configure.ac
ParaFly-0.1.0/depcomp
ParaFly-0.1.0/install-sh
ParaFly-0.1.0/missing
ParaFly-0.1.0/src/
ParaFly-0.1.0/src/.deps/
ParaFly-0.1.0/src/.deps/ParaFly.Po
ParaFly-0.1.0/src/.deps/argProcessor.Po
ParaFly-0.1.0/src/Makefile
ParaFly-0.1.0/src/Makefile.am
ParaFly-0.1.0/src/Makefile.in
ParaFly-0.1.0/src/ParaFly.cpp
ParaFly-0.1.0/src/argProcessor.cpp
ParaFly-0.1.0/src/argProcessor.hpp
ParaFly-0.1.0/stamp-h1
ParaFly-0.1.0/test/
ParaFly-0.1.0/test/Makefile
ParaFly-0.1.0/test/cmds.txt
ParaFly-0.1.0/test/rand_exit.pl
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for library containing cos... none required
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
make[2]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0'
Making install in src
make[3]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0/src'
g++ -DHAVE_CONFIG_H -I. -I..    -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -MT ParaFly.o -MD -MP -MF .deps/ParaFly.Tpo -c -o ParaFly.o ParaFly.cpp
mv -f .deps/ParaFly.Tpo .deps/ParaFly.Po
g++ -DHAVE_CONFIG_H -I. -I..    -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2 -MT argProcessor.o -MD -MP -MF .deps/argProcessor.Tpo -c -o argProcessor.o argProcessor.cpp
mv -f .deps/argProcessor.Tpo .deps/argProcessor.Po
g++ -pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated -m64 -g -O2   -o ParaFly ParaFly.o argProcessor.o 
make[4]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0/src'
test -z "/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0/bin" || /bin/mkdir -p "/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0/bin"
  /usr/bin/install -c ParaFly '/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0/bin'
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0/src'
make[3]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0/src'
make[3]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0'
make[4]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0'
make[3]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0'
make[2]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/ParaFly-0.1.0'
ln -sf Trimmomatic-0.36 Trimmomatic
tar xvf samtools-1.3.1.tar.bz2
samtools-1.3.1/
samtools-1.3.1/aclocal.m4
samtools-1.3.1/AUTHORS
samtools-1.3.1/bam.c
samtools-1.3.1/bam.h
samtools-1.3.1/bam2bcf.c
samtools-1.3.1/bam2bcf.h
samtools-1.3.1/bam2bcf_indel.c
samtools-1.3.1/bam2depth.c
samtools-1.3.1/bam_addrprg.c
samtools-1.3.1/bam_aux.c
samtools-1.3.1/bam_cat.c
samtools-1.3.1/bam_color.c
samtools-1.3.1/bam_endian.h
samtools-1.3.1/bam_flags.c
samtools-1.3.1/bam_import.c
samtools-1.3.1/bam_index.c
samtools-1.3.1/bam_lpileup.c
samtools-1.3.1/bam_lpileup.h
samtools-1.3.1/bam_mate.c
samtools-1.3.1/bam_md.c
samtools-1.3.1/bam_plbuf.c
samtools-1.3.1/bam_plbuf.h
samtools-1.3.1/bam_plcmd.c
samtools-1.3.1/bam_quickcheck.c
samtools-1.3.1/bam_reheader.c
samtools-1.3.1/bam_rmdup.c
samtools-1.3.1/bam_rmdupse.c
samtools-1.3.1/bam_sort.c
samtools-1.3.1/bam_split.c
samtools-1.3.1/bam_stat.c
samtools-1.3.1/bam_tview.c
samtools-1.3.1/bam_tview.h
samtools-1.3.1/bam_tview_curses.c
samtools-1.3.1/bam_tview_html.c
samtools-1.3.1/bamshuf.c
samtools-1.3.1/bamtk.c
samtools-1.3.1/bedcov.c
samtools-1.3.1/bedidx.c
samtools-1.3.1/ChangeLog.old
samtools-1.3.1/config.h.in
samtools-1.3.1/config.mk.in
samtools-1.3.1/configure
samtools-1.3.1/configure.ac
samtools-1.3.1/cut_target.c
samtools-1.3.1/dict.c
samtools-1.3.1/errmod.c
samtools-1.3.1/errmod.h
samtools-1.3.1/examples/
samtools-1.3.1/faidx.c
samtools-1.3.1/htslib-1.3.1/
samtools-1.3.1/INSTALL
samtools-1.3.1/install-sh
samtools-1.3.1/kprobaln.c
samtools-1.3.1/kprobaln.h
samtools-1.3.1/LICENSE
samtools-1.3.1/Makefile
samtools-1.3.1/Makefile.mingw
samtools-1.3.1/misc/
samtools-1.3.1/NEWS
samtools-1.3.1/padding.c
samtools-1.3.1/phase.c
samtools-1.3.1/README
samtools-1.3.1/sam.c
samtools-1.3.1/sam.h
samtools-1.3.1/sam_header.c
samtools-1.3.1/sam_header.h
samtools-1.3.1/sam_opts.c
samtools-1.3.1/sam_opts.h
samtools-1.3.1/sam_view.c
samtools-1.3.1/sample.c
samtools-1.3.1/sample.h
samtools-1.3.1/samtools.1
samtools-1.3.1/samtools.h
samtools-1.3.1/stats.c
samtools-1.3.1/stats_isize.c
samtools-1.3.1/stats_isize.h
samtools-1.3.1/test/
samtools-1.3.1/win32/
samtools-1.3.1/win32/libcurses.a
samtools-1.3.1/win32/libz.a
samtools-1.3.1/win32/xcurses.h
samtools-1.3.1/win32/zconf.h
samtools-1.3.1/win32/zlib.h
samtools-1.3.1/test/addrprg/
samtools-1.3.1/test/bam2fq/
samtools-1.3.1/test/dat/
samtools-1.3.1/test/fixmate/
samtools-1.3.1/test/idxstats/
samtools-1.3.1/test/merge/
samtools-1.3.1/test/mpileup/
samtools-1.3.1/test/quickcheck/
samtools-1.3.1/test/reheader/
samtools-1.3.1/test/split/
samtools-1.3.1/test/stat/
samtools-1.3.1/test/test.c
samtools-1.3.1/test/test.h
samtools-1.3.1/test/test.pl
samtools-1.3.1/test/tview/
samtools-1.3.1/test/vcf-miniview.c
samtools-1.3.1/test/tview/test_get_rg_sample.c
samtools-1.3.1/test/stat/1.stats.expected
samtools-1.3.1/test/stat/10.stats.expected
samtools-1.3.1/test/stat/10_map_cigar.sam
samtools-1.3.1/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat
samtools-1.3.1/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat
samtools-1.3.1/test/stat/1_map_cigar.sam
samtools-1.3.1/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat
samtools-1.3.1/test/stat/2.stats.expected
samtools-1.3.1/test/stat/2_equal_cigar_full_seq.sam
samtools-1.3.1/test/stat/3.stats.expected
samtools-1.3.1/test/stat/3_map_cigar_equal_seq.sam
samtools-1.3.1/test/stat/4.stats.expected
samtools-1.3.1/test/stat/4_X_cigar_full_seq.sam
samtools-1.3.1/test/stat/5.stats.expected
samtools-1.3.1/test/stat/5_insert_cigar.sam
samtools-1.3.1/test/stat/6.stats.expected
samtools-1.3.1/test/stat/7.stats.expected
samtools-1.3.1/test/stat/7_supp.sam
samtools-1.3.1/test/stat/8.stats.expected
samtools-1.3.1/test/stat/8_secondary.sam
samtools-1.3.1/test/stat/9.stats.expected
samtools-1.3.1/test/stat/test.fa
samtools-1.3.1/test/stat/test.fa.fai
samtools-1.3.1/test/split/test_count_rg.c
samtools-1.3.1/test/split/test_expand_format_string.c
samtools-1.3.1/test/split/test_filter_header_rg.c
samtools-1.3.1/test/split/test_parse_args.c
samtools-1.3.1/test/reheader/1_view1.sam.expected
samtools-1.3.1/test/reheader/1_view1.sam.expected.err
samtools-1.3.1/test/reheader/2_view1.sam.expected
samtools-1.3.1/test/reheader/2_view1.sam.expected.err
samtools-1.3.1/test/reheader/3_view1.sam.expected
samtools-1.3.1/test/reheader/3_view1.sam.expected.err
samtools-1.3.1/test/reheader/hdr.sam
samtools-1.3.1/test/quickcheck/1.quickcheck.badeof.bam
samtools-1.3.1/test/quickcheck/2.quickcheck.badheader.bam
samtools-1.3.1/test/quickcheck/3.quickcheck.ok.bam
samtools-1.3.1/test/quickcheck/4.quickcheck.ok.bam
samtools-1.3.1/test/quickcheck/5.quickcheck.truncated.cram
samtools-1.3.1/test/quickcheck/all.expected
samtools-1.3.1/test/mpileup/1read.bam
samtools-1.3.1/test/mpileup/1read.sam
samtools-1.3.1/test/mpileup/anomalous.sam
samtools-1.3.1/test/mpileup/c1#clip.bam
samtools-1.3.1/test/mpileup/c1#ID.bam
samtools-1.3.1/test/mpileup/c1#ID2.bam
samtools-1.3.1/test/mpileup/c1#pad1.bam
samtools-1.3.1/test/mpileup/c1#pad2.bam
samtools-1.3.1/test/mpileup/c1#pad3.bam
samtools-1.3.1/test/mpileup/c1.fa
samtools-1.3.1/test/mpileup/c1.fa.fai
samtools-1.3.1/test/mpileup/ce#5b.bam
samtools-1.3.1/test/mpileup/ce#5b.bam.bai
samtools-1.3.1/test/mpileup/ce#5b.cram
samtools-1.3.1/test/mpileup/ce#5b.cram.crai
samtools-1.3.1/test/mpileup/ce#5b.sam
samtools-1.3.1/test/mpileup/ce#large_seq.bam
samtools-1.3.1/test/mpileup/ce#unmap.bam
samtools-1.3.1/test/mpileup/ce#unmap1.bam
samtools-1.3.1/test/mpileup/ce#unmap2.bam
samtools-1.3.1/test/mpileup/ce.fa
samtools-1.3.1/test/mpileup/ce.fa.fai
samtools-1.3.1/test/mpileup/deep.sam
samtools-1.3.1/test/mpileup/depth.reg
samtools-1.3.1/test/mpileup/expected/
samtools-1.3.1/test/mpileup/indels.sam
samtools-1.3.1/test/mpileup/md5/
samtools-1.3.1/test/mpileup/mpileup-E.bam
samtools-1.3.1/test/mpileup/mpileup.1.bam
samtools-1.3.1/test/mpileup/mpileup.1.bam.bai
samtools-1.3.1/test/mpileup/mpileup.2.bam
samtools-1.3.1/test/mpileup/mpileup.3.bam
samtools-1.3.1/test/mpileup/mpileup.ref.fa
samtools-1.3.1/test/mpileup/mpileup.ref.fa.fai
samtools-1.3.1/test/mpileup/mpileup.reg
samtools-1.3.1/test/mpileup/overlap50.sam
samtools-1.3.1/test/mpileup/overlapIllumina.bam
samtools-1.3.1/test/mpileup/regions
samtools-1.3.1/test/mpileup/regression.sh
samtools-1.3.1/test/mpileup/xx#depth1.sam
samtools-1.3.1/test/mpileup/xx#depth2.sam
samtools-1.3.1/test/mpileup/xx#minimal.bam
samtools-1.3.1/test/mpileup/xx#triplet.bam
samtools-1.3.1/test/mpileup/xx.bed
samtools-1.3.1/test/mpileup/xx.bed2
samtools-1.3.1/test/mpileup/xx.fa
samtools-1.3.1/test/mpileup/xx.fa.fai
samtools-1.3.1/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
samtools-1.3.1/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
samtools-1.3.1/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
samtools-1.3.1/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
samtools-1.3.1/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
samtools-1.3.1/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
samtools-1.3.1/test/mpileup/expected/1.out.f3-6.gz
samtools-1.3.1/test/mpileup/expected/10.out
samtools-1.3.1/test/mpileup/expected/11.out
samtools-1.3.1/test/mpileup/expected/12.out
samtools-1.3.1/test/mpileup/expected/13.out
samtools-1.3.1/test/mpileup/expected/14.out
samtools-1.3.1/test/mpileup/expected/15.out
samtools-1.3.1/test/mpileup/expected/16.out
samtools-1.3.1/test/mpileup/expected/17.out
samtools-1.3.1/test/mpileup/expected/18.out
samtools-1.3.1/test/mpileup/expected/19.out
samtools-1.3.1/test/mpileup/expected/2.out
samtools-1.3.1/test/mpileup/expected/20.out
samtools-1.3.1/test/mpileup/expected/21.out
samtools-1.3.1/test/mpileup/expected/22.out
samtools-1.3.1/test/mpileup/expected/23.out
samtools-1.3.1/test/mpileup/expected/24.out
samtools-1.3.1/test/mpileup/expected/25.out
samtools-1.3.1/test/mpileup/expected/26.out
samtools-1.3.1/test/mpileup/expected/27.out
samtools-1.3.1/test/mpileup/expected/28.out
samtools-1.3.1/test/mpileup/expected/29.out
samtools-1.3.1/test/mpileup/expected/3.out
samtools-1.3.1/test/mpileup/expected/30.out
samtools-1.3.1/test/mpileup/expected/31.out
samtools-1.3.1/test/mpileup/expected/32.out
samtools-1.3.1/test/mpileup/expected/33.out
samtools-1.3.1/test/mpileup/expected/34.out
samtools-1.3.1/test/mpileup/expected/35.out
samtools-1.3.1/test/mpileup/expected/37.out
samtools-1.3.1/test/mpileup/expected/38.out
samtools-1.3.1/test/mpileup/expected/39.out
samtools-1.3.1/test/mpileup/expected/4.out
samtools-1.3.1/test/mpileup/expected/40.out
samtools-1.3.1/test/mpileup/expected/41.out
samtools-1.3.1/test/mpileup/expected/42.out
samtools-1.3.1/test/mpileup/expected/43.out
samtools-1.3.1/test/mpileup/expected/44.out
samtools-1.3.1/test/mpileup/expected/45.out
samtools-1.3.1/test/mpileup/expected/46.out
samtools-1.3.1/test/mpileup/expected/47.out
samtools-1.3.1/test/mpileup/expected/48.out
samtools-1.3.1/test/mpileup/expected/49.out
samtools-1.3.1/test/mpileup/expected/5.out
samtools-1.3.1/test/mpileup/expected/50.out
samtools-1.3.1/test/mpileup/expected/51.out
samtools-1.3.1/test/mpileup/expected/52.out
samtools-1.3.1/test/mpileup/expected/53.out
samtools-1.3.1/test/mpileup/expected/54.out
samtools-1.3.1/test/mpileup/expected/55.out
samtools-1.3.1/test/mpileup/expected/56.out
samtools-1.3.1/test/mpileup/expected/57.out
samtools-1.3.1/test/mpileup/expected/58.out
samtools-1.3.1/test/mpileup/expected/59.out
samtools-1.3.1/test/mpileup/expected/6.out
samtools-1.3.1/test/mpileup/expected/60.out
samtools-1.3.1/test/mpileup/expected/61.out
samtools-1.3.1/test/mpileup/expected/62.out
samtools-1.3.1/test/mpileup/expected/63.out
samtools-1.3.1/test/mpileup/expected/64.out
samtools-1.3.1/test/mpileup/expected/65.out
samtools-1.3.1/test/mpileup/expected/66.out
samtools-1.3.1/test/mpileup/expected/67.out
samtools-1.3.1/test/mpileup/expected/68.out
samtools-1.3.1/test/mpileup/expected/69.out
samtools-1.3.1/test/mpileup/expected/7.out
samtools-1.3.1/test/mpileup/expected/70.out
samtools-1.3.1/test/mpileup/expected/71.out
samtools-1.3.1/test/mpileup/expected/72.out
samtools-1.3.1/test/mpileup/expected/73.out
samtools-1.3.1/test/mpileup/expected/74.out
samtools-1.3.1/test/mpileup/expected/75.out
samtools-1.3.1/test/mpileup/expected/76.out
samtools-1.3.1/test/mpileup/expected/77.out
samtools-1.3.1/test/mpileup/expected/8.out
samtools-1.3.1/test/mpileup/expected/9.out
samtools-1.3.1/test/mpileup/expected/d1_1.out
samtools-1.3.1/test/mpileup/expected/d1_12.out
samtools-1.3.1/test/mpileup/expected/d1_2.out
samtools-1.3.1/test/mpileup/expected/d2_12r.out
samtools-1.3.1/test/mpileup/expected/d3_12.out
samtools-1.3.1/test/mpileup/expected/d3_12r1a.out
samtools-1.3.1/test/mpileup/expected/d3_12r2a.out
samtools-1.3.1/test/mpileup/expected/d4_12.out
samtools-1.3.1/test/mpileup/expected/d4_12b.out
samtools-1.3.1/test/mpileup/expected/d4_12r.out
samtools-1.3.1/test/merge/2.merge.expected.bam
samtools-1.3.1/test/merge/3.merge.expected.bam
samtools-1.3.1/test/merge/3.merge.expected.err
samtools-1.3.1/test/merge/4.merge.expected.bam
samtools-1.3.1/test/merge/5.merge.expected.bam
samtools-1.3.1/test/merge/5.merge.expected.sam
samtools-1.3.1/test/merge/6.merge.expected.bam
samtools-1.3.1/test/merge/7.merge.expected.bam
samtools-1.3.1/test/merge/test_3.fofn
samtools-1.3.1/test/merge/test_bam_translate.c
samtools-1.3.1/test/merge/test_header.sam
samtools-1.3.1/test/merge/test_rtrans_build.c
samtools-1.3.1/test/merge/test_trans_tbl_init.c
samtools-1.3.1/test/idxstats/test_input_1_a.bam.expected
samtools-1.3.1/test/idxstats/test_input_1_a.bam.expected.err
samtools-1.3.1/test/fixmate/1_coord_sort.sam
samtools-1.3.1/test/fixmate/1_coord_sort.sam.expected
samtools-1.3.1/test/fixmate/1_coord_sort.sam.expected.err
samtools-1.3.1/test/fixmate/2_isize_overflow.sam
samtools-1.3.1/test/fixmate/2_isize_overflow.sam.expected
samtools-1.3.1/test/fixmate/3_reverse_read_pp_lt.sam
samtools-1.3.1/test/fixmate/3_reverse_read_pp_lt.sam.expected
samtools-1.3.1/test/fixmate/4_reverse_read_pp_equal.sam
samtools-1.3.1/test/fixmate/4_reverse_read_pp_equal.sam.expected
samtools-1.3.1/test/fixmate/5_ct.sam
samtools-1.3.1/test/fixmate/5_ct.sam.expected
samtools-1.3.1/test/fixmate/6_ct_replace.sam
samtools-1.3.1/test/fixmate/6_ct_replace.sam.expected
samtools-1.3.1/test/dat/bam2fq.001.sam
samtools-1.3.1/test/dat/bam2fq.002.sam
samtools-1.3.1/test/dat/bam2fq.003.sam
samtools-1.3.1/test/dat/cat.hdr
samtools-1.3.1/test/dat/cram_md5/
samtools-1.3.1/test/dat/depad.001.fa
samtools-1.3.1/test/dat/depad.001.fa.fai
samtools-1.3.1/test/dat/depad.001p.sam
samtools-1.3.1/test/dat/depad.001u.sam
samtools-1.3.1/test/dat/dict.fa
samtools-1.3.1/test/dat/dict.out
samtools-1.3.1/test/dat/empty.expected
samtools-1.3.1/test/dat/large_chrom.out
samtools-1.3.1/test/dat/large_chrom.sam
samtools-1.3.1/test/dat/large_chrom_bai_index.err
samtools-1.3.1/test/dat/mpileup.1.sam
samtools-1.3.1/test/dat/mpileup.2.sam
samtools-1.3.1/test/dat/mpileup.3.sam
samtools-1.3.1/test/dat/mpileup.err.1
samtools-1.3.1/test/dat/mpileup.out.1
samtools-1.3.1/test/dat/mpileup.out.2
samtools-1.3.1/test/dat/mpileup.out.3
samtools-1.3.1/test/dat/mpileup.out.4
samtools-1.3.1/test/dat/mpileup.ref.fa
samtools-1.3.1/test/dat/mpileup.ref.fa.fai
samtools-1.3.1/test/dat/test_input_1_a.bam
samtools-1.3.1/test/dat/test_input_1_a.bam.bai.expected
samtools-1.3.1/test/dat/test_input_1_a.sam
samtools-1.3.1/test/dat/test_input_1_a_regex.sam
samtools-1.3.1/test/dat/test_input_1_b.bam
samtools-1.3.1/test/dat/test_input_1_b.sam
samtools-1.3.1/test/dat/test_input_1_b_regex.sam
samtools-1.3.1/test/dat/test_input_1_c.bam
samtools-1.3.1/test/dat/test_input_1_c.sam
samtools-1.3.1/test/dat/view.001.01.bed
samtools-1.3.1/test/dat/view.001.02.bed
samtools-1.3.1/test/dat/view.001.fa
samtools-1.3.1/test/dat/view.001.fa.fai
samtools-1.3.1/test/dat/view.001.sam
samtools-1.3.1/test/dat/view.002.01.bed
samtools-1.3.1/test/dat/view.002.02.bed
samtools-1.3.1/test/dat/view.002.fa
samtools-1.3.1/test/dat/view.002.fa.fai
samtools-1.3.1/test/dat/view.002.sam
samtools-1.3.1/test/dat/view.003.expected.sam
samtools-1.3.1/test/dat/view.003.sam
samtools-1.3.1/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
samtools-1.3.1/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
samtools-1.3.1/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
samtools-1.3.1/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
samtools-1.3.1/test/bam2fq/1.1.fq.expected
samtools-1.3.1/test/bam2fq/1.2.fq.expected
samtools-1.3.1/test/bam2fq/1.stdout.expected
samtools-1.3.1/test/bam2fq/2.1.fq.expected
samtools-1.3.1/test/bam2fq/2.2.fq.expected
samtools-1.3.1/test/bam2fq/2.s.fq.expected
samtools-1.3.1/test/bam2fq/2.stdout.expected
samtools-1.3.1/test/bam2fq/3.1.fq.expected
samtools-1.3.1/test/bam2fq/3.2.fq.expected
samtools-1.3.1/test/bam2fq/3.s.fq.expected
samtools-1.3.1/test/bam2fq/3.stdout.expected
samtools-1.3.1/test/bam2fq/4.1.fq.expected
samtools-1.3.1/test/bam2fq/4.2.fq.expected
samtools-1.3.1/test/bam2fq/4.s.fq.expected
samtools-1.3.1/test/bam2fq/4.stdout.expected
samtools-1.3.1/test/addrprg/1_fixup.sam
samtools-1.3.1/test/addrprg/1_fixup.sam.expected
samtools-1.3.1/test/addrprg/1_fixup.sam.expected.err
samtools-1.3.1/test/addrprg/2_fixup_orphan.sam
samtools-1.3.1/test/addrprg/2_fixup_orphan.sam.expected
samtools-1.3.1/test/addrprg/2_fixup_orphan.sam.expected.err
samtools-1.3.1/test/addrprg/3_fixup.sam.expected
samtools-1.3.1/test/addrprg/3_fixup.sam.expected.err
samtools-1.3.1/test/addrprg/4_fixup_norg.sam
samtools-1.3.1/test/addrprg/4_fixup_norg.sam.expected
samtools-1.3.1/test/addrprg/4_fixup_norg.sam.expected.err
samtools-1.3.1/misc/ace2sam.c
samtools-1.3.1/misc/blast2sam.pl
samtools-1.3.1/misc/bowtie2sam.pl
samtools-1.3.1/misc/export2sam.pl
samtools-1.3.1/misc/HmmGlocal.java
samtools-1.3.1/misc/interpolate_sam.pl
samtools-1.3.1/misc/maq2sam.c
samtools-1.3.1/misc/md5fa.c
samtools-1.3.1/misc/md5sum-lite.c
samtools-1.3.1/misc/novo2sam.pl
samtools-1.3.1/misc/plot-bamstats
samtools-1.3.1/misc/psl2sam.pl
samtools-1.3.1/misc/r2plot.lua
samtools-1.3.1/misc/sam2vcf.pl
samtools-1.3.1/misc/samtools.pl
samtools-1.3.1/misc/seq_cache_populate.pl
samtools-1.3.1/misc/soap2sam.pl
samtools-1.3.1/misc/varfilter.py
samtools-1.3.1/misc/vcfutils.lua
samtools-1.3.1/misc/wgsim.1
samtools-1.3.1/misc/wgsim.c
samtools-1.3.1/misc/wgsim_eval.pl
samtools-1.3.1/misc/zoom2sam.pl
samtools-1.3.1/htslib-1.3.1/bgzf.c
samtools-1.3.1/htslib-1.3.1/bgzip.c
samtools-1.3.1/htslib-1.3.1/config.h.in
samtools-1.3.1/htslib-1.3.1/config.mk.in
samtools-1.3.1/htslib-1.3.1/configure
samtools-1.3.1/htslib-1.3.1/configure.ac
samtools-1.3.1/htslib-1.3.1/cram/
samtools-1.3.1/htslib-1.3.1/faidx.5
samtools-1.3.1/htslib-1.3.1/faidx.c
samtools-1.3.1/htslib-1.3.1/hfile.c
samtools-1.3.1/htslib-1.3.1/hfile_internal.h
samtools-1.3.1/htslib-1.3.1/hfile_irods.c
samtools-1.3.1/htslib-1.3.1/hfile_libcurl.c
samtools-1.3.1/htslib-1.3.1/hfile_net.c
samtools-1.3.1/htslib-1.3.1/hts.c
samtools-1.3.1/htslib-1.3.1/hts_internal.h
samtools-1.3.1/htslib-1.3.1/htsfile.1
samtools-1.3.1/htslib-1.3.1/htsfile.c
samtools-1.3.1/htslib-1.3.1/htslib/
samtools-1.3.1/htslib-1.3.1/htslib.mk
samtools-1.3.1/htslib-1.3.1/htslib.pc.in
samtools-1.3.1/htslib-1.3.1/htslib_vars.mk
samtools-1.3.1/htslib-1.3.1/INSTALL
samtools-1.3.1/htslib-1.3.1/kfunc.c
samtools-1.3.1/htslib-1.3.1/knetfile.c
samtools-1.3.1/htslib-1.3.1/kstring.c
samtools-1.3.1/htslib-1.3.1/LICENSE
samtools-1.3.1/htslib-1.3.1/Makefile
samtools-1.3.1/htslib-1.3.1/md5.c
samtools-1.3.1/htslib-1.3.1/NEWS
samtools-1.3.1/htslib-1.3.1/plugin.c
samtools-1.3.1/htslib-1.3.1/README
samtools-1.3.1/htslib-1.3.1/regidx.c
samtools-1.3.1/htslib-1.3.1/sam.5
samtools-1.3.1/htslib-1.3.1/sam.c
samtools-1.3.1/htslib-1.3.1/synced_bcf_reader.c
samtools-1.3.1/htslib-1.3.1/tabix.1
samtools-1.3.1/htslib-1.3.1/tabix.c
samtools-1.3.1/htslib-1.3.1/tbx.c
samtools-1.3.1/htslib-1.3.1/test/
samtools-1.3.1/htslib-1.3.1/vcf.5
samtools-1.3.1/htslib-1.3.1/vcf.c
samtools-1.3.1/htslib-1.3.1/vcf_sweep.c
samtools-1.3.1/htslib-1.3.1/vcfutils.c
samtools-1.3.1/htslib-1.3.1/test/aux#aux_java.cram
samtools-1.3.1/htslib-1.3.1/test/auxf#values.sam
samtools-1.3.1/htslib-1.3.1/test/auxf.fa
samtools-1.3.1/htslib-1.3.1/test/auxf.fa.fai
samtools-1.3.1/htslib-1.3.1/test/c1#bounds.sam
samtools-1.3.1/htslib-1.3.1/test/c1#clip.sam
samtools-1.3.1/htslib-1.3.1/test/c1#noseq.sam
samtools-1.3.1/htslib-1.3.1/test/c1#pad1.sam
samtools-1.3.1/htslib-1.3.1/test/c1#pad2.sam
samtools-1.3.1/htslib-1.3.1/test/c1#pad3.sam
samtools-1.3.1/htslib-1.3.1/test/c1#unknown.sam
samtools-1.3.1/htslib-1.3.1/test/c1.fa
samtools-1.3.1/htslib-1.3.1/test/c1.fa.fai
samtools-1.3.1/htslib-1.3.1/test/c2#pad.sam
samtools-1.3.1/htslib-1.3.1/test/c2.fa
samtools-1.3.1/htslib-1.3.1/test/c2.fa.fai
samtools-1.3.1/htslib-1.3.1/test/ce#1.sam
samtools-1.3.1/htslib-1.3.1/test/ce#2.sam
samtools-1.3.1/htslib-1.3.1/test/ce#5.sam
samtools-1.3.1/htslib-1.3.1/test/ce#5b.sam
samtools-1.3.1/htslib-1.3.1/test/ce#5b_java.cram
samtools-1.3.1/htslib-1.3.1/test/ce#large_seq.sam
samtools-1.3.1/htslib-1.3.1/test/ce#supp.sam
samtools-1.3.1/htslib-1.3.1/test/ce#tag_depadded.sam
samtools-1.3.1/htslib-1.3.1/test/ce#tag_padded.sam
samtools-1.3.1/htslib-1.3.1/test/ce#unmap.sam
samtools-1.3.1/htslib-1.3.1/test/ce#unmap1.sam
samtools-1.3.1/htslib-1.3.1/test/ce#unmap2.sam
samtools-1.3.1/htslib-1.3.1/test/ce.fa
samtools-1.3.1/htslib-1.3.1/test/ce.fa.fai
samtools-1.3.1/htslib-1.3.1/test/compare_sam.pl
samtools-1.3.1/htslib-1.3.1/test/cross_validate.sh
samtools-1.3.1/htslib-1.3.1/test/faidx.fa
samtools-1.3.1/htslib-1.3.1/test/fieldarith.c
samtools-1.3.1/htslib-1.3.1/test/fieldarith.sam
samtools-1.3.1/htslib-1.3.1/test/formatcols.vcf
samtools-1.3.1/htslib-1.3.1/test/hfile.c
samtools-1.3.1/htslib-1.3.1/test/noroundtrip-out.vcf
samtools-1.3.1/htslib-1.3.1/test/noroundtrip.vcf
samtools-1.3.1/htslib-1.3.1/test/sam.c
samtools-1.3.1/htslib-1.3.1/test/test-regidx.c
samtools-1.3.1/htslib-1.3.1/test/test-vcf-api.c
samtools-1.3.1/htslib-1.3.1/test/test-vcf-api.out
samtools-1.3.1/htslib-1.3.1/test/test-vcf-hdr-in.vcf
samtools-1.3.1/htslib-1.3.1/test/test-vcf-hdr.out
samtools-1.3.1/htslib-1.3.1/test/test-vcf-sweep.c
samtools-1.3.1/htslib-1.3.1/test/test-vcf-sweep.out
samtools-1.3.1/htslib-1.3.1/test/test.pl
samtools-1.3.1/htslib-1.3.1/test/test_view.c
samtools-1.3.1/htslib-1.3.1/test/xx#blank.sam
samtools-1.3.1/htslib-1.3.1/test/xx#large_aux.sam
samtools-1.3.1/htslib-1.3.1/test/xx#large_aux2.sam
samtools-1.3.1/htslib-1.3.1/test/xx#large_aux_java.cram
samtools-1.3.1/htslib-1.3.1/test/xx#minimal.sam
samtools-1.3.1/htslib-1.3.1/test/xx#pair.sam
samtools-1.3.1/htslib-1.3.1/test/xx#repeated.sam
samtools-1.3.1/htslib-1.3.1/test/xx#rg.sam
samtools-1.3.1/htslib-1.3.1/test/xx#tlen.sam
samtools-1.3.1/htslib-1.3.1/test/xx#tlen2.sam
samtools-1.3.1/htslib-1.3.1/test/xx#triplet.sam
samtools-1.3.1/htslib-1.3.1/test/xx#unsorted.sam
samtools-1.3.1/htslib-1.3.1/test/xx.fa
samtools-1.3.1/htslib-1.3.1/test/xx.fa.fai
samtools-1.3.1/htslib-1.3.1/htslib/bgzf.h
samtools-1.3.1/htslib-1.3.1/htslib/cram.h
samtools-1.3.1/htslib-1.3.1/htslib/faidx.h
samtools-1.3.1/htslib-1.3.1/htslib/hfile.h
samtools-1.3.1/htslib-1.3.1/htslib/hts.h
samtools-1.3.1/htslib-1.3.1/htslib/hts_defs.h
samtools-1.3.1/htslib-1.3.1/htslib/kbitset.h
samtools-1.3.1/htslib-1.3.1/htslib/kfunc.h
samtools-1.3.1/htslib-1.3.1/htslib/khash.h
samtools-1.3.1/htslib-1.3.1/htslib/khash_str2int.h
samtools-1.3.1/htslib-1.3.1/htslib/klist.h
samtools-1.3.1/htslib-1.3.1/htslib/knetfile.h
samtools-1.3.1/htslib-1.3.1/htslib/kseq.h
samtools-1.3.1/htslib-1.3.1/htslib/ksort.h
samtools-1.3.1/htslib-1.3.1/htslib/kstring.h
samtools-1.3.1/htslib-1.3.1/htslib/regidx.h
samtools-1.3.1/htslib-1.3.1/htslib/sam.h
samtools-1.3.1/htslib-1.3.1/htslib/synced_bcf_reader.h
samtools-1.3.1/htslib-1.3.1/htslib/tbx.h
samtools-1.3.1/htslib-1.3.1/htslib/vcf.h
samtools-1.3.1/htslib-1.3.1/htslib/vcf_sweep.h
samtools-1.3.1/htslib-1.3.1/htslib/vcfutils.h
samtools-1.3.1/htslib-1.3.1/cram/cram.h
samtools-1.3.1/htslib-1.3.1/cram/cram_codecs.c
samtools-1.3.1/htslib-1.3.1/cram/cram_codecs.h
samtools-1.3.1/htslib-1.3.1/cram/cram_decode.c
samtools-1.3.1/htslib-1.3.1/cram/cram_decode.h
samtools-1.3.1/htslib-1.3.1/cram/cram_encode.c
samtools-1.3.1/htslib-1.3.1/cram/cram_encode.h
samtools-1.3.1/htslib-1.3.1/cram/cram_external.c
samtools-1.3.1/htslib-1.3.1/cram/cram_index.c
samtools-1.3.1/htslib-1.3.1/cram/cram_index.h
samtools-1.3.1/htslib-1.3.1/cram/cram_io.c
samtools-1.3.1/htslib-1.3.1/cram/cram_io.h
samtools-1.3.1/htslib-1.3.1/cram/cram_samtools.c
samtools-1.3.1/htslib-1.3.1/cram/cram_samtools.h
samtools-1.3.1/htslib-1.3.1/cram/cram_stats.c
samtools-1.3.1/htslib-1.3.1/cram/cram_stats.h
samtools-1.3.1/htslib-1.3.1/cram/cram_structs.h
samtools-1.3.1/htslib-1.3.1/cram/files.c
samtools-1.3.1/htslib-1.3.1/cram/mFILE.c
samtools-1.3.1/htslib-1.3.1/cram/mFILE.h
samtools-1.3.1/htslib-1.3.1/cram/misc.h
samtools-1.3.1/htslib-1.3.1/cram/open_trace_file.c
samtools-1.3.1/htslib-1.3.1/cram/open_trace_file.h
samtools-1.3.1/htslib-1.3.1/cram/os.h
samtools-1.3.1/htslib-1.3.1/cram/pooled_alloc.c
samtools-1.3.1/htslib-1.3.1/cram/pooled_alloc.h
samtools-1.3.1/htslib-1.3.1/cram/rANS_byte.h
samtools-1.3.1/htslib-1.3.1/cram/rANS_static.c
samtools-1.3.1/htslib-1.3.1/cram/rANS_static.h
samtools-1.3.1/htslib-1.3.1/cram/sam_header.c
samtools-1.3.1/htslib-1.3.1/cram/sam_header.h
samtools-1.3.1/htslib-1.3.1/cram/string_alloc.c
samtools-1.3.1/htslib-1.3.1/cram/string_alloc.h
samtools-1.3.1/htslib-1.3.1/cram/thread_pool.c
samtools-1.3.1/htslib-1.3.1/cram/thread_pool.h
samtools-1.3.1/htslib-1.3.1/cram/vlen.c
samtools-1.3.1/htslib-1.3.1/cram/vlen.h
samtools-1.3.1/htslib-1.3.1/cram/zfio.c
samtools-1.3.1/htslib-1.3.1/cram/zfio.h
samtools-1.3.1/examples/00README.txt
samtools-1.3.1/examples/ex1.fa
samtools-1.3.1/examples/ex1.sam.gz
samtools-1.3.1/examples/toy.fa
samtools-1.3.1/examples/toy.sam
cd samtools-1.3.1 && ./configure --without-curses --prefix=`pwd`
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking location of HTSlib source tree... htslib-1.3.1
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
config.status: config.h is unchanged
=== configuring in htslib-1.3.1 (/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/samtools-1.3.1/htslib-1.3.1)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/samtools-1.3.1'  '--without-curses' --cache-file=/dev/null --srcdir=.
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
config.status: config.h is unchanged
cd samtools-1.3.1 && make
make[2]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/samtools-1.3.1'
gcc -pthread -rdynamic   -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libbam.a htslib-1.3.1/libhts.a  -lm -lz -ldl
make[2]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins/samtools-1.3.1'
mv samtools-1.3.1/samtools ./BIN/.
make[1]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.1/trinity-plugins'
sh ./util/support_scripts/trinity_install_tests.sh
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Performing Unit Tests of Build
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JellyFish:               has been Installed Properly
Inchworm:                has been Installed Properly
Chrysalis Installation appears to have FAILED
QuantifyGraph Installation appears to have FAILED
GraphFromFasta Installation appears to have FAILED
ReadsToTranscripts Installation appears to have FAILED
parafly:                 has been Installed Properly
samtools          has been Installed Properly

[Chen Dong]

Some additional information of the Java, gcc and bowtie2.
$ bowtie2 --version
/home/user/myBins/bowtie2-2.2.9/bowtie2-align-s version 2.2.9
64-bit
Built on localhost.localdomain
Thu Apr 21 18:36:37 EDT 2016
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-54)
Options: -O3 -m64 -msse2  -funroll-loops -g3 -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
$ java -version
openjdk version "1.8.0_141"
OpenJDK Runtime Environment (build 1.8.0_141-b16)
OpenJDK 64-Bit Server VM (build 25.141-b16, mixed mode)

[Brian Haas]

Hi,

You might need to update to GCC version 4.9 or higher.   I'm currently using 5.1 (on linux) and 5.3 (on mac) - no particular preference here, just using what's installed.

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Chen Dong]

Thanks Brian for the reply. gcc is 4.9 now as you can see. Still, the same problem. Please advise. Thank you!

Performing Unit Tests of Build
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
JellyFish:               has been Installed Properly
Inchworm:                has been Installed Properly
Chrysalis Installation appears to have FAILED
QuantifyGraph Installation appears to have FAILED
GraphFromFasta Installation appears to have FAILED
ReadsToTranscripts Installation appears to have FAILED
parafly:                 has been Installed Properly
samtools          has been Installed Properly

[yGu@pw25-32allxbi trinityrnaseq-Trinity-v2.5.1]$ gcc --version
gcc (GCC) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[yGu@pw25-32allxbi trinityrnaseq-Trinity-v2.5.1]$ java -version

openjdk version "1.8.0_141"
OpenJDK Runtime Environment (build 1.8.0_141-b16)
OpenJDK 64-Bit Server VM (build 25.141-b16, mixed mode)

[yGu@pw25-32allxbi trinityrnaseq-Trinity-v2.5.1]$

On Tuesday, October 24, 2017 at 5:26:15 PM UTC-7, Chen Dong wrote:

[Brian Haas]

hmm....  

is it still the error:  ./MakeDepend: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found 

also, did you type 'make clean' followed by 'make' ?

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[Chen Dong]

Yes. I did make once more and the error message is the same.  ./MakeDepend: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found 

 Then I did make clean as shown below.
$ make clean
cd Inchworm && make clean
make[1]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/Inchworm'
Making clean in src
make[2]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/Inchworm/src'
test -z "inchworm cigar_tweaker pull_reads_with_kmers FastaToDeBruijn fastaToKmerCoverageStats" || rm -f inchworm cigar_tweaker pull_reads_with_kmers FastaToDeBruijn fastaToKmerCoverageStats
rm -f *.o
make[2]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/Inchworm/src'
Making clean in .
make[2]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/Inchworm'
make[2]: Nothing to be done for `clean-am'.
make[2]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/Inchworm'
make[1]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/Inchworm'
cd Chrysalis && make clean UNSUPPORTED=yes

./MakeDepend: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./MakeDepend)
make[1]: *** [depend] Error 1

make[1]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/Chrysalis'
for file in ; do rm -f ./$file; done
rm -f MakeDepend ./MakeDepend contigs.out my.permanent.log.file \
             core a.out Makefile.bak bsubin BasevectorTables.h ./checkLock
find obj -name '*.o' -exec rm {} \; || /bin/true
find: `obj': No such file or directory
rm -rf cxx_repository
rm -f lib_*_temp.a
make[1]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/Chrysalis'
cd trinity-plugins && make clean
make[1]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/trinity-plugins'
rm -rf "jellyfish-2.2.6" ./jellyfish # has tar.gz
rm -rf ./seqtk-trinity-0.0.2
rm -rf ./samtools-1.3.1/
cd scaffold_iworm_contigs && make clean
make[2]: Entering directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/trinity-plugins/scaffold_iworm_contigs'
rm -f scaffold_iworm_contigs
make[2]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/trinity-plugins/scaffold_iworm_contigs'
cd parafly-code && make clean
/bin/sh: line 0: cd: parafly-code: No such file or directory
make[1]: *** [clean] Error 1
make[1]: Leaving directory `/home/arcadeo/myBins/trinityrnaseq-Trinity-v2.5.0/trinity-plugins'
make: *** [clean] Error 2

...

[Brian Haas]

It might be that other system components need to be upgraded:

https://stackoverflow.com/questions/44773296/libstdc-so-6-version-glibcxx-3-4-20-not-found

there are a few other helpful posts from googling the error.

best,

~b

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