Re: CTAT-LR-Fusion make error

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Brian Haas

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May 15, 2024, 9:43:48 AM5/15/24

to Yuyun Zhang, Trinity_CTAT_users

Hi,

We have docker and singularity images available in case that's an option for you:

https://github.com/TrinityCTAT/CTAT-LR-fusion/wiki/ctat_lr_fusion_docker_and_singularity

Otherwise, the perl module 'Set-IntervalTree' is available here:
https://metacpan.org/pod/Set::IntervalTree

and you can try to install that separately as needed.

On Wed, May 15, 2024 at 9:39 AM Yuyun Zhang <zhangy...@gmail.com> wrote:

Hi,

I plan to use CTAT_LR_fusion to detect fusion transcripts in my datasets. But I can't compile it. Could you please help me with resolving this issue? Here is the error:

$ make

cd ctat-minimap2 && make
make[1]: Entering directory '/u/project/gxxiao/gxxiao5/yuyun/software/CTAT-LR-fusion.v0.13.0/ctat-minimap2'
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC main.c -o main.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kthread.c -o kthread.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC kalloc.c -o kalloc.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC misc.c -o misc.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC bseq.c -o bseq.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sketch.c -o sketch.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC sdust.c -o sdust.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC options.c -o options.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC index.c -o index.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC lchain.c -o lchain.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC align.c -o align.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC hit.c -o hit.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC seed.c -o seed.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC map.c -o map.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC format.c -o format.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC pe.c -o pe.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC esterr.c -o esterr.o
cc -c -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC splitidx.c -o splitidx.o
cc -c -g -Wall -O2 -Wc++-compat -msse2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o
cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o
cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o
cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o
cc -c -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o
cc -c -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o
cc -c -g -Wall -O2 -Wc++-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o
cc -c -g -Wall -O2 -Wc++-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o
ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
cc -g -Wall -O2 -Wc++-compat main.o -o ctat-minimap2 -L. -lminimap2 -lm -lz -lpthread
make[1]: Leaving directory '/u/project/gxxiao/gxxiao5/yuyun/software/CTAT-LR-fusion.v0.13.0/ctat-minimap2'
cd plugins && make
make[1]: Entering directory '/u/project/gxxiao/gxxiao5/yuyun/software/CTAT-LR-fusion.v0.13.0/plugins'
tar xvf Set-IntervalTree-0.01.tar.gz && \
cd Set-IntervalTree-0.01 && \
perl Makefile.PL && \
make && \
mv lib/Set ../../PerlLib/ && \
mv blib/arch/auto ../../PerlLib && \
mv blib/lib/auto/Set/IntervalTree/autosplit.ix ../../PerlLib/auto/Set/IntervalTree/.
Set-IntervalTree-0.01/
Set-IntervalTree-0.01/src/
Set-IntervalTree-0.01/src/Makefile
Set-IntervalTree-0.01/src/interval_tree.h
Set-IntervalTree-0.01/src/test_main.cc
Set-IntervalTree-0.01/lib/
Set-IntervalTree-0.01/lib/Set/
Set-IntervalTree-0.01/lib/Set/IntervalTree.pm
Set-IntervalTree-0.01/Changes
Set-IntervalTree-0.01/MANIFEST
Set-IntervalTree-0.01/t/
Set-IntervalTree-0.01/t/Set-IntervalTree.t
Set-IntervalTree-0.01/typemap
Set-IntervalTree-0.01/perlobject.map
Set-IntervalTree-0.01/IntervalTree.xs
Set-IntervalTree-0.01/Makefile.PL
Set-IntervalTree-0.01/README
Set-IntervalTree-0.01/META.yml
Generating a Unix-style Makefile
Writing Makefile for Set::IntervalTree
Writing MYMETA.yml and MYMETA.json
make[2]: Entering directory '/u/project/gxxiao/gxxiao5/yuyun/software/CTAT-LR-fusion.v0.13.0/plugins/Set-IntervalTree-0.01'
cp lib/Set/IntervalTree.pm blib/lib/Set/IntervalTree.pm
AutoSplitting blib/lib/Set/IntervalTree.pm (blib/lib/auto/Set/IntervalTree)
Running Mkbootstrap for IntervalTree ()
chmod 644 "IntervalTree.bs"
"/u/project/gxxiao/gxxiao5/yuyun/miniconda/envs/yuyun/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- IntervalTree.bs blib/arch/auto/Set/IntervalTree/IntervalTree.bs 644
"/u/project/gxxiao/gxxiao5/yuyun/miniconda/envs/yuyun/bin/perl" "/u/project/gxxiao/gxxiao5/yuyun/miniconda/envs/yuyun/lib/perl5/core_perl/ExtUtils/xsubpp" -C++ -typemap '/u/project/gxxiao/gxxiao5/yuyun/miniconda/envs/yuyun/lib/perl5/core_perl/ExtUtils/typemap' -typemap '/u/project/gxxiao/gxxiao5/yuyun/software/CTAT-LR-fusion.v0.13.0/plugins/Set-IntervalTree-0.01/perlobject.map' -typemap '/u/project/gxxiao/gxxiao5/yuyun/software/CTAT-LR-fusion.v0.13.0/plugins/Set-IntervalTree-0.01/typemap' IntervalTree.xs > IntervalTree.xsc
mv IntervalTree.xsc IntervalTree.c
g++ -c -Isrc -D_REENTRANT -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /u/project/gxxiao/gxxiao5/yuyun/miniconda/envs/yuyun/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/perl_1703310062586/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=/u/project/gxxiao/gxxiao5/yuyun/miniconda/envs/yuyun=/usr/local/src/conda-prefix -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O0 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC --sysroot=/u/project/gxxiao/gxxiao5/yuyun/miniconda/envs/yuyun/bin/..//x86_64-conda-linux-gnu/sysroot "-I/u/project/gxxiao/gxxiao5/yuyun/miniconda/envs/yuyun/lib/perl5/5.32/core_perl/CORE" -Isrc IntervalTree.c
g++: error: unrecognized command line option ‘-fno-plt’
make[2]: *** [Makefile:342: IntervalTree.o] Error 1
make[2]: Leaving directory '/u/project/gxxiao/gxxiao5/yuyun/software/CTAT-LR-fusion.v0.13.0/plugins/Set-IntervalTree-0.01'
make[1]: *** [Makefile:3: all] Error 2
make[1]: Leaving directory '/u/project/gxxiao/gxxiao5/yuyun/software/CTAT-LR-fusion.v0.13.0/plugins'
make: *** [Makefile:7: plugins_only] Error 2

Thank you!
Yuyun

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