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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Installation problems #103

Open francicco opened 4 years ago

francicco commented 4 years ago

Hi,

I'm reinstalling cactus due to conflict in the environment. I recompiled the kyoto libraries. Now what I did was

git clone https://github.com/ComparativeGenomicsToolkit/cactus.git
cd cactus
cd submodules && ln -s /mnt/storage/scratch/tk19812/software/clapack/ clapack (recompiled) && cd ..
virtualenv cactus_env
source cactus_env/bin/activate
pip install biopython boto3 coveralls cython deap ete3 gffutils graphviz matplotlib networkx numpy PyPDF2 pysam pytest pytest-cov PyYAML scipy seaborn 
pip install --upgrade toil

here I got this error:

Collecting actualSonLib (from progressiveCactus==1.0)
  ERROR: Could not find a version that satisfies the requirement actualSonLib (from progressiveCactus==1.0) (from versions: none)
ERROR: No matching distribution found for actualSonLib (from progressiveCactus==1.0)

then I did:

git submodule update --init
make
Building dependency sonLib
Building dependency pinchesAndCacti
Building dependency matchingAndOrdering
Building dependency cPecan
Building dependency hdf5
Building dependency hal

During hal I get this error:

inc/halPhyloP.h:16:24: fatal error: tree_model.h: No such file or directory

How should I fix this? Thanks a lot F

diekhans commented 4 years ago

tree_model.h is part of phylop, please make sure phast is in the correct location or disable phast/philop support.

Francesco Cicconardi notifications@github.com writes:

Hi,

I'm reinstalling cactus due to conflict in the environment. I recompiled the kyoto libraries. Now what I did was

git clone https://github.com/ComparativeGenomicsToolkit/cactus.git
cd cactus
cd submodules && ln -s /mnt/storage/scratch/tk19812/software/clapack/ clapack (recompiled) && cd ..
virtualenv cactus_env
source cactus_env/bin/activate
pip install biopython boto3 coveralls cython deap ete3 gffutils graphviz matplotlib networkx numpy PyPDF2 pysam pytest pytest-cov PyYAML scipy seaborn 
pip install --upgrade toil

here I got this error:

Collecting actualSonLib (from progressiveCactus==1.0)
  ERROR: Could not find a version that satisfies the requirement actualSonLib (from progressiveCactus==1.0) (from versions: none)
ERROR: No matching distribution found for actualSonLib (from progressiveCactus==1.0)

then I did:

git submodule update --init
make
Building dependency sonLib
Building dependency pinchesAndCacti
Building dependency matchingAndOrdering
Building dependency cPecan
Building dependency hdf5
Building dependency hal

During hal I get this error:

inc/halPhyloP.h:16:24: fatal error: tree_model.h: No such file or directory

How should I fix this? Thanks a lot F

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103 Hi,

I'm reinstalling cactus due to conflict in the environment. I recompiled the kyoto libraries. Now what I did was

git clone https://github.com/ComparativeGenomicsToolkit/cactus.git cd cactus cd submodules && ln -s /mnt/storage/scratch/tk19812/software/clapack/ clapack (recompiled) && cd .. virtualenv cactus_env source cactus_env/bin/activate pip install biopython boto3 coveralls cython deap ete3 gffutils graphviz matplotlib networkx numpy PyPDF2 pysam pytest pytest-cov PyYAML scipy seaborn pip install --upgrade toil

here I got this error:

Collecting actualSonLib (from progressiveCactus==1.0) ERROR: Could not find a version that satisfies the requirement actualSonLib (from progressiveCactus==1.0) (from versions: none) ERROR: No matching distribution found for actualSonLib (from progressiveCactus==1.0)

then I did:

git submodule update --init make Building dependency sonLib Building dependency pinchesAndCacti Building dependency matchingAndOrdering Building dependency cPecan Building dependency hdf5 Building dependency hal

During hal I get this error:

inc/halPhyloP.h:16:24: fatal error: tree_model.h: No such file or directory

How should I fix this? Thanks a lot F

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francicco commented 4 years ago

I guess with git submodule update --init I download everything, right? F

francicco commented 4 years ago

I'm also get error while compiling modify

h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -fPIC -I ../lib/ -o ../bin//halRemoveGenome halRemoveGenome.cpp markAncestors.o ../lib//halLib.a ..//../sonLib/lib/sonLib.a ..//../sonLib/lib/cuTest.a
hdf5_impl/hdf5Alignment.cpp:168: error: undefined reference to 'H5::H5File::flush(H5F_scope_t) const'
hdf5_impl/hdf5MetaData.cpp:97: error: undefined reference to 'H5::H5Object::getNumAttrs() const'
hdf5_impl/hdf5MetaData.cpp:99: error: undefined reference to 'H5::H5Object::iterateAttrs(void (*)(H5::H5Object&, std::string, void*), unsigned int*, void*)'
hdf5_impl/hdf5MetaData.cpp:73: error: undefined reference to 'H5::H5Object::openAttribute(std::string const&) const'
hdf5_impl/hdf5MetaData.cpp:121: error: undefined reference to 'H5::H5Object::createAttribute(std::string const&, H5::DataType const&, H5::DataSpace const&, H5::PropList const&) const'
hdf5_impl/hdf5MetaData.cpp:119: error: undefined reference to 'H5::H5Object::removeAttr(char const*) const'
collect2: error: ld returned 1 exit status
make: *** [../bin//halRemoveGenome] Error 1

Please, I think I need help F

francicco commented 4 years ago

But assuming both submodules are compiled still the cactus binary is not generated. F

diekhans commented 4 years ago

What version of HDF5 do you have?

Francesco Cicconardi notifications@github.com writes:

I'm also get error while compiling modify

h5c++  -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -fPIC -I ../lib/ -o ../bin//halRemoveGenome halRemoveGenome.cpp markAncestors.o ../lib//halLib.a ..//../sonLib/lib/sonLib.a ..//../sonLib/lib/cuTest.a
hdf5_impl/hdf5Alignment.cpp:168: error: undefined reference to 'H5::H5File::flush(H5F_scope_t) const'
hdf5_impl/hdf5MetaData.cpp:97: error: undefined reference to 'H5::H5Object::getNumAttrs() const'
hdf5_impl/hdf5MetaData.cpp:99: error: undefined reference to 'H5::H5Object::iterateAttrs(void (*)(H5::H5Object&, std::string, void*), unsigned int*, void*)'
hdf5_impl/hdf5MetaData.cpp:73: error: undefined reference to 'H5::H5Object::openAttribute(std::string const&) const'
hdf5_impl/hdf5MetaData.cpp:121: error: undefined reference to 'H5::H5Object::createAttribute(std::string const&, H5::DataType const&, H5::DataSpace const&, H5::PropList const&) const'
hdf5_impl/hdf5MetaData.cpp:119: error: undefined reference to 'H5::H5Object::removeAttr(char const*) const'
collect2: error: ld returned 1 exit status
make: *** [../bin//halRemoveGenome] Error 1

Please, I think I need help F

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-541421904 I'm also get error while compiling modify

h5c++ -O3 -g -Wall -funroll-loops -DNDEBUG -I..//../sonLib/lib -fPIC -I ../lib/ -o ../bin//halRemoveGenome halRemoveGenome.cpp markAncestors.o ../lib//halLib.a ..//../sonLib/lib/sonLib.a ..//../sonLib/lib/cuTest.a hdf5_impl/hdf5Alignment.cpp:168: error: undefined reference to 'H5::H5File::flush(H5F_scope_t) const' hdf5_impl/hdf5MetaData.cpp:97: error: undefined reference to 'H5::H5Object::getNumAttrs() const' hdf5_impl/hdf5MetaData.cpp:99: error: undefined reference to 'H5::H5Object::iterateAttrs(void ()(H5::H5Object&, std::string, void), unsigned int, void)' hdf5_impl/hdf5MetaData.cpp:73: error: undefined reference to 'H5::H5Object::openAttribute(std::string const&) const' hdf5_impl/hdf5MetaData.cpp:121: error: undefined reference to 'H5::H5Object::createAttribute(std::string const&, H5::DataType const&, H5::DataSpace const&, H5::PropList const&) const' hdf5_impl/hdf5MetaData.cpp:119: error: undefined reference to 'H5::H5Object::removeAttr(char const*) const' collect2: error: ld returned 1 exit status make: *** [../bin//halRemoveGenome] Error 1

Please, I think I need help F

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diekhans commented 4 years ago

I am going to try to reproduce your installation problems.

What OS are you using?

francicco commented 4 years ago

The HDF5 is the 1.8.16-foss-2016a. I'm on a cluster, how do I check the OS?

Thanks F

diekhans commented 4 years ago

Ask your sysadmins would probably be best way to get OS and release, as the way to check for specific linux version varies.

Francesco Cicconardi notifications@github.com writes:

The HDF5 is the 1.8.16-foss-2016a. I'm on a cluster, how do I check the OS?

Thanks F

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-542089405 The HDF5 is the 1.8.16-foss-2016a. I'm on a cluster, how do I check the OS?

Thanks F

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francicco commented 4 years ago

CentOS Linux release 7.3.1611 (Core)

diekhans commented 4 years ago

The above error appears to an install error with the HDF5 C++ support. It isn't finding the library files. This would be in libhdf5_cpp.so* of libhdf5_cpp.a.

However, the fact that HAL compiled means it found the include files.

you can try run that h5c++ command by hand and add the -echo option to see where it is looking for the libraries.

francicco commented 4 years ago

I'm still struggling with the h5c

h5c++  -MM -MT ../objs/api/impl/halAlignmentInstance.o -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I../../clapack/INCLUDE -I../../clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halAlignmentInstance.cpp >impl/halAlignmentInstance.depend -echo
+ test xyes = xyes
+ test xyes '!=' xyes
+ eval g++ -I/home/tk19812/software/hdf5-1.10.6/include -MM -MT ../objs/api/impl/halAlignmentInstance.o -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I../../clapack/INCLUDE -I../../clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halAlignmentInstance.cpp
++ g++ -I/home/tk19812/software/hdf5-1.10.6/include -MM -MT ../objs/api/impl/halAlignmentInstance.o -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I../../clapack/INCLUDE -I../../clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -c impl/halAlignmentInstance.cpp
In file included from hdf5_impl/hdf5Genome.h:15,
                 from hdf5_impl/hdf5Alignment.h:13,
                 from impl/halAlignmentInstance.cpp:11:
hdf5_impl/hdf5ExternalArray.h:17:18: error: missing binary operator before token "("
   17 | #if H5_VERSION_GE(1, 10, 1)
      |                  ^
+ status=1
+ test 1 '!=' 0
+ exit 1
glennhickey commented 4 years ago

That's pretty mysterious. It's saying the H5_VERSION_GE macro is undefined. Maybe somehow it's not included in <H5Cpp.h> for you? If that's it, you could try sticking an #include <hdf5.h> at the top of hal/api/hdf5_impl/hdf5ExternalArray.h and if that works we can update the repo.

Otherwise, if apt is an option, you can install hdf5 as described in the Dockerfile. 1.10.6 (from your log) is newer than the version I'm using (10.0) but there's no indication in the docs that anything's changed https://confluence.hdfgroup.org/display/HDF5/H5_VERSION_GE

francicco commented 4 years ago 
fatal error: H5Cpp.h: No such file or directory
   12 | #include <H5Cpp.h>

I'll try to install the 10.0 F

francicco commented 4 years ago

Possibly the binary isn't rightfully compiled? F

diekhans commented 4 years ago

are you able to use docker? That way you can avoid compiling.

another thing you can try is seeing if you can compile the HDF5 C++ examples: https://support.hdfgroup.org/HDF5/examples/cpp-src.html

with h5c++

francicco commented 4 years ago

I'm on a cluster, I think I can't directly use docker. F

francicco commented 4 years ago

I tried this way from the examples:

h5c++ writedata.cpp 
writedata.cpp:32:10: fatal error: H5Cpp.h: No such file or directory
   32 | #include "H5Cpp.h"
      |          ^~~~~~~~~
compilation terminated.
diekhans commented 4 years ago

something is wrong with your HDF5 C++ support install.

francicco commented 4 years ago

Ok @diekhans,

I fix that issue, now I'm facing this problem:

h5c++  -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I../../clapack/INCLUDE -I../../clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -I tests -o ../bin/halHdf5Tests ../objs/api/hdf5_tests/hdf5SegmentTypeTest.o ../objs/api/hdf5_tests/hdf5ExternalArrayTest.o ../objs/api/hdf5_tests/allTests.o ../objs/api/hdf5_tests/hdf5SequenceTypeTest.o ../objs/api/hdf5_tests/hdf5DnaTypeTest.o ../objs/api/hdf5_tests/hdf5Test.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a -L../../phast/lib -lphast -L../../clapack -L../../clapack/F2CLIBS -llapack -ltmg -lblaswr -lf2c 
/usr/bin/ld: cannot find -lphast
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -ltmg
/usr/bin/ld: cannot find -lblaswr
/usr/bin/ld: cannot find -lf2c

Are these other dependecies? Cheers F

francicco commented 4 years ago

Ok, did that, now I got:

make[4]: *** No rule to make target/home/tk19812/software/cactus_kyoto_branch/submodules/sonLib/lib/stPinchesAndCacti.a', needed by ../bin//stCafTests'. Stop.

francicco commented 4 years ago

it seems like it worked

make suball1
make[1]: Entering directory `/home/tk19812/software/cactus'
#cd submodules/kyoto && KT_OPTIONS=--disable-lua make PREFIX=/home/tk19812/software/cactus && make install
#cd submodules/sonLib && PKG_CONFIG_PATH=/home/tk19812/software/cactus/lib/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig make
#mkdir -p bin
#ln -f submodules/sonLib/bin/[a-zA-Z]* bin/
cd submodules/cPecan && make
make[2]: Entering directory `/home/tk19812/software/cactus/submodules/cPecan'
cd externalTools && make all
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools'
cd lastz-distrib-1.03.54 && make install
make[4]: Entering directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54'
cd src && make install
make[5]: Entering directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54/src'
install -d      ../../../../sonLib/bin
install lastz   ../../../../sonLib/bin
install lastz_D ../../../../sonLib/bin
make[5]: Leaving directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54/src'
make[4]: Leaving directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54'
mv /home/tk19812/software/cactus/submodules/sonLib/bin/lastz /home/tk19812/software/cactus/submodules/sonLib/bin/cPecanLastz
mv /home/tk19812/software/cactus/submodules/sonLib/bin/lastz_D /home/tk19812/software/cactus/submodules/sonLib/bin/cPecanLastz_D
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools'
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/cPecan'
cd submodules/hal &&  make
make[2]: Entering directory `/home/tk19812/software/cactus/submodules/hal'
cd api && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/api'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/api'
cd stats && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/stats'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/stats'
cd randgen && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/randgen'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/randgen'
cd validate && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/validate'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/validate'
cd mutations && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/mutations'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/mutations'
cd fasta && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/fasta'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/fasta'
cd alignmentDepth && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
cd liftover && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/liftover'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/liftover'
cd lod && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/lod'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/lod'
cd maf && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/maf'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/maf'
cd blockViz && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
cd extract && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/extract'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/extract'
cd analysis && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/analysis'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/analysis'
cd phyloP && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
cd modify && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/modify'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/modify'
cd assemblyHub && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
cd synteny && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/synteny'
cd api && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/api'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/api'
cd stats && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/stats'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/stats'
cd randgen && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/randgen'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/randgen'
cd validate && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/validate'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/validate'
cd mutations && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/mutations'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/mutations'
cd fasta && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/fasta'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/fasta'
cd alignmentDepth && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
cd liftover && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/liftover'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/liftover'
cd lod && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/lod'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/lod'
cd maf && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/maf'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/maf'
cd blockViz && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
cd extract && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/extract'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/extract'
cd analysis && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/analysis'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/analysis'
cd phyloP && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
cd modify && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/modify'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/modify'
cd assemblyHub && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
cd synteny && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/hal'
mkdir -p bin
ln -f submodules/hal/bin/* bin/
ln -f submodules/hal/lib/libHal.a submodules/hal/lib/halLib.a
#cd submodules/matchingAndOrdering && make
#cd submodules/pinchesAndCacti && make
make[1]: Leaving directory `/home/tk19812/software/cactus'
make all_libs
make[1]: Entering directory `/home/tk19812/software/cactus'
make all_libs.api all_libs.setup all_libs.blastLib all_libs.caf all_libs.bar all_libs.blast all_libs.normalisation all_libs.hal all_libs.phylogeny all_libs.reference all_libs.faces all_libs.check all_libs.pipeline all_libs.preprocessor all_libs.hal all_libs.dbTest
make[2]: Entering directory `/home/tk19812/software/cactus'
cd api && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/api'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/api'
cd setup && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/setup'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/setup'
cd blastLib && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/blastLib'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blastLib'
cd caf && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/caf'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/caf'
cd bar && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/bar'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/bar'
cd blast && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/blast'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blast'
cd normalisation && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/normalisation'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/normalisation'
cd hal && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/hal'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/hal'
cd phylogeny && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/phylogeny'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/phylogeny'
cd reference && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/reference'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/reference'
cd faces && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/faces'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/faces'
cd check && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/check'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/check'
cd pipeline && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/pipeline'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/pipeline'
cd preprocessor && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/preprocessor'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/preprocessor'
make[2]: `all_libs.hal' is up to date.
cd dbTest && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/dbTest'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/dbTest'
make[2]: Leaving directory `/home/tk19812/software/cactus'
make[1]: Leaving directory `/home/tk19812/software/cactus'
make all_progs
make[1]: Entering directory `/home/tk19812/software/cactus'
make all_libs.api all_libs.setup all_libs.blastLib all_libs.caf all_libs.bar all_libs.blast all_libs.normalisation all_libs.hal all_libs.phylogeny all_libs.reference all_libs.faces all_libs.check all_libs.pipeline all_libs.preprocessor all_libs.hal all_libs.dbTest
make[2]: Entering directory `/home/tk19812/software/cactus'
cd api && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/api'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/api'
cd setup && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/setup'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/setup'
cd blastLib && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/blastLib'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blastLib'
cd caf && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/caf'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/caf'
cd bar && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/bar'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/bar'
cd blast && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/blast'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blast'
cd normalisation && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/normalisation'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/normalisation'
cd hal && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/hal'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/hal'
cd phylogeny && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/phylogeny'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/phylogeny'
cd reference && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/reference'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/reference'
cd faces && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/faces'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/faces'
cd check && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/check'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/check'
cd pipeline && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/pipeline'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/pipeline'
cd preprocessor && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/preprocessor'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/preprocessor'
make[2]: `all_libs.hal' is up to date.
cd dbTest && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/dbTest'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/dbTest'
make[2]: Leaving directory `/home/tk19812/software/cactus'
make all_progs.api all_progs.setup all_progs.blastLib all_progs.caf all_progs.bar all_progs.blast all_progs.normalisation all_progs.hal all_progs.phylogeny all_progs.reference all_progs.faces all_progs.check all_progs.pipeline all_progs.preprocessor all_progs.hal all_progs.dbTest
make[2]: Entering directory `/home/tk19812/software/cactus'
cd api && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/api'
make ../bin//cactusAPITests 
make[4]: Entering directory `/home/tk19812/software/cactus/api'
make[4]: `../bin//cactusAPITests' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/api'
make[3]: Leaving directory `/home/tk19812/software/cactus/api'
cd setup && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/setup'
make ../bin//cactus_setup  
make[4]: Entering directory `/home/tk19812/software/cactus/setup'
make[4]: `../bin//cactus_setup' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/setup'
make[3]: Leaving directory `/home/tk19812/software/cactus/setup'
cd blastLib && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/blastLib'
make[3]: Nothing to be done for `all_progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blastLib'
cd caf && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/caf'
make ../bin//stCafTests ../bin//cactus_caf
make[4]: Entering directory `/home/tk19812/software/cactus/caf'
make[4]: `../bin//stCafTests' is up to date.
make[4]: `../bin//cactus_caf' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/caf'
make[3]: Leaving directory `/home/tk19812/software/cactus/caf'
cd bar && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/bar'
make ../bin//cactus_bar ../bin//cactus_barTests
make[4]: Entering directory `/home/tk19812/software/cactus/bar'
make[4]: `../bin//cactus_bar' is up to date.
make[4]: `../bin//cactus_barTests' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/bar'
make[3]: Leaving directory `/home/tk19812/software/cactus/bar'
cd blast && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/blast'
make ../bin//cactus_convertAlignmentsToInternalNames ../bin//cactus_stripUniqueIDs ../bin//cactus_blast_convertCoordinates ../bin//cactus_blast_chunkSequences ../bin//cactus_blast_chunkFlowerSequences ../bin//cactus_blast_sortAlignments ../bin//cactus_calculateMappingQualities ../bin//cactus_mirrorAndOrientAlignments ../bin//cactus_splitAlignmentOverlaps ../bin//cactus_coverage
make[4]: Entering directory `/home/tk19812/software/cactus/blast'
make[4]: `../bin//cactus_convertAlignmentsToInternalNames' is up to date.
make[4]: `../bin//cactus_stripUniqueIDs' is up to date.
make[4]: `../bin//cactus_blast_convertCoordinates' is up to date.
make[4]: `../bin//cactus_blast_chunkSequences' is up to date.
make[4]: `../bin//cactus_blast_chunkFlowerSequences' is up to date.
make[4]: `../bin//cactus_blast_sortAlignments' is up to date.
make[4]: `../bin//cactus_calculateMappingQualities' is up to date.
make[4]: `../bin//cactus_mirrorAndOrientAlignments' is up to date.
make[4]: `../bin//cactus_splitAlignmentOverlaps' is up to date.
make[4]: `../bin//cactus_coverage' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/blast'
make[3]: Leaving directory `/home/tk19812/software/cactus/blast'
cd normalisation && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/normalisation'
make ../bin//cactus_normalisation
make[4]: Entering directory `/home/tk19812/software/cactus/normalisation'
make[4]: `../bin//cactus_normalisation' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/normalisation'
make[3]: Leaving directory `/home/tk19812/software/cactus/normalisation'
cd hal && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/hal'
make ../bin//cactus_halGenerator ../bin//cactus_halGeneratorTests ../bin//cactus_fastaGenerator
make[4]: Entering directory `/home/tk19812/software/cactus/hal'
make[4]: `../bin//cactus_halGenerator' is up to date.
make[4]: `../bin//cactus_halGeneratorTests' is up to date.
make[4]: `../bin//cactus_fastaGenerator' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/hal'
make[3]: Leaving directory `/home/tk19812/software/cactus/hal'
cd phylogeny && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/phylogeny'
make ../bin//cactus_phylogeny 
make[4]: Entering directory `/home/tk19812/software/cactus/phylogeny'
make[4]: `../bin//cactus_phylogeny' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/phylogeny'
make[3]: Leaving directory `/home/tk19812/software/cactus/phylogeny'
cd reference && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/reference'
make ../bin//cactus_reference ../bin//cactus_addReferenceCoordinates ../bin//referenceTests ../bin//cactus_getReferenceSeq
make[4]: Entering directory `/home/tk19812/software/cactus/reference'
make[4]: `../bin//cactus_reference' is up to date.
make[4]: `../bin//cactus_addReferenceCoordinates' is up to date.
make[4]: `../bin//referenceTests' is up to date.
make[4]: `../bin//cactus_getReferenceSeq' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/reference'
make[3]: Leaving directory `/home/tk19812/software/cactus/reference'
cd faces && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/faces'
make ../bin//cactus_fillAdjacencies
make[4]: Entering directory `/home/tk19812/software/cactus/faces'
make[4]: `../bin//cactus_fillAdjacencies' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/faces'
make[3]: Leaving directory `/home/tk19812/software/cactus/faces'
cd check && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/check'
make ../bin//cactus_check 
make[4]: Entering directory `/home/tk19812/software/cactus/check'
make[4]: `../bin//cactus_check' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/check'
make[3]: Leaving directory `/home/tk19812/software/cactus/check'
cd pipeline && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/pipeline'
make ../bin//cactus_workflow_getFlowers ../bin//cactus_workflow_extendFlowers ../bin//cactus_workflow_flowerStats ../bin//cactus_workflow_convertAlignmentCoordinates ../bin//cactus_secondaryDatabase ../bin//docker_test_script
make[4]: Entering directory `/home/tk19812/software/cactus/pipeline'
make[4]: `../bin//cactus_workflow_getFlowers' is up to date.
make[4]: `../bin//cactus_workflow_extendFlowers' is up to date.
make[4]: `../bin//cactus_workflow_flowerStats' is up to date.
make[4]: `../bin//cactus_workflow_convertAlignmentCoordinates' is up to date.
make[4]: `../bin//cactus_secondaryDatabase' is up to date.
make[4]: `../bin//docker_test_script' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/pipeline'
make[3]: Leaving directory `/home/tk19812/software/cactus/pipeline'
cd preprocessor && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/preprocessor'
make ../bin//cactus_analyseAssembly ../bin//cactus_batch_mergeChunks ../bin//cactus_makeAlphaNumericHeaders.py ../bin//cactus_filterSmallFastaSequences.py
make[4]: Entering directory `/home/tk19812/software/cactus/preprocessor'
make[4]: `../bin//cactus_analyseAssembly' is up to date.
make[4]: `../bin//cactus_batch_mergeChunks' is up to date.
make[4]: `../bin//cactus_makeAlphaNumericHeaders.py' is up to date.
make[4]: `../bin//cactus_filterSmallFastaSequences.py' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/preprocessor'
cd lastzRepeatMasking && make all
make[4]: Entering directory `/home/tk19812/software/cactus/preprocessor/lastzRepeatMasking'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/home/tk19812/software/cactus/preprocessor/lastzRepeatMasking'
make[3]: Leaving directory `/home/tk19812/software/cactus/preprocessor'
make[2]: `all_progs.hal' is up to date.
cd dbTest && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/dbTest'
make ../bin//dbTestScript 
make[4]: Entering directory `/home/tk19812/software/cactus/dbTest'
make[4]: `../bin//dbTestScript' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/dbTest'
make[3]: Leaving directory `/home/tk19812/software/cactus/dbTest'
make[2]: Leaving directory `/home/tk19812/software/cactus'
make[1]: Leaving directory `/home/tk19812/software/cactus'
make suball2
make[1]: Entering directory `/home/tk19812/software/cactus'
#cd submodules/kyoto && KT_OPTIONS=--disable-lua make PREFIX=/home/tk19812/software/cactus && make install
#cd submodules/sonLib && PKG_CONFIG_PATH=/home/tk19812/software/cactus/lib/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig make
#mkdir -p bin
#ln -f submodules/sonLib/bin/[a-zA-Z]* bin/
cd submodules/hal &&  make
make[2]: Entering directory `/home/tk19812/software/cactus/submodules/hal'
cd api && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/api'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/api'
cd stats && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/stats'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/stats'
cd randgen && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/randgen'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/randgen'
cd validate && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/validate'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/validate'
cd mutations && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/mutations'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/mutations'
cd fasta && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/fasta'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/fasta'
cd alignmentDepth && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
cd liftover && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/liftover'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/liftover'
cd lod && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/lod'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/lod'
cd maf && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/maf'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/maf'
cd blockViz && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
cd extract && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/extract'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/extract'
cd analysis && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/analysis'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/analysis'
cd phyloP && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
cd modify && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/modify'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/modify'
cd assemblyHub && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
cd synteny && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/synteny'
cd api && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/api'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/api'
cd stats && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/stats'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/stats'
cd randgen && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/randgen'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/randgen'
cd validate && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/validate'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/validate'
cd mutations && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/mutations'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/mutations'
cd fasta && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/fasta'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/fasta'
cd alignmentDepth && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
cd liftover && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/liftover'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/liftover'
cd lod && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/lod'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/lod'
cd maf && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/maf'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/maf'
cd blockViz && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
cd extract && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/extract'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/extract'
cd analysis && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/analysis'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/analysis'
cd phyloP && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
cd modify && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/modify'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/modify'
cd assemblyHub && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
cd synteny && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/hal'
mkdir -p bin
ln -f submodules/hal/bin/* bin/
ln -f submodules/hal/lib/libHal.a submodules/hal/lib/halLib.a
cd api && make all_libs
make[2]: Entering directory `/home/tk19812/software/cactus/api'
make[2]: Nothing to be done for `all_libs'.
make[2]: Leaving directory `/home/tk19812/software/cactus/api'
cd submodules/cactus2hal && make
make[2]: Entering directory `/home/tk19812/software/cactus/submodules/cactus2hal'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/cactus2hal'
mkdir -p bin
ln -f submodules/cactus2hal/bin/* bin/
make[1]: Leaving directory `/home/tk19812/software/cactus'

but I can't see the cactus binary in the bin folder F

francicco commented 4 years ago 
(cactus_env) [tk19812@bp1-login01 cactus]$ cactus_env/bin/cactus jobStore examples/evolverMammals.txt examples/evolverMammals.hal --root mr --binariesMode local
Using config from path /home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/cactus_progressive_config.xml.
('simHuman_chr6', True, False)
('simMouse_chr6', True, True)
('simRat_chr6', True, True)
('mr', False, True)
('Anc1', False, False)
('simCow_chr6', True, False)
('simDog_chr6', True, False)
('Anc2', False, False)
('Anc0', False, False)
['Anc1', 'Anc2', 'Anc0']
xmlRoot = <multi_cactus inputSequenceNames="simHuman_chr6 simMouse_chr6 simRat_chr6 simCow_chr6 simDog_chr6" inputSequences="/home/tk19812/software/cactus/examples/simHuman.chr6 /home/tk19812/software/cactus/examples/simMouse.chr6 /home/tk19812/software/cactus/examples/simRat.chr6 /home/tk19812/software/cactus/examples/simCow.chr6 /home/tk19812/software/cactus/examples/simDog.chr6">
    <tree>(simMouse_chr6:0.084509,simRat_chr6:0.091589,simCow_chr6:0.514545,simDog_chr6:0.488495,simHuman_chr6:0.41599200000000003)mr;</tree>
    <cactus experiment_path="/tmp/tmp2non1lhe/progressiveAlignment/mr/mr_experiment.xml" name="mr" />
</multi_cactus>
Limiting maxCores to CPU count of system (48).
Limiting maxMemory to physically available memory (404143419392).
Limiting maxDisk to physically available disk (19227271168).
Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
Issued job 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instanced4_i1jqv with job batch system ID: 0 and cores: 1, disk: 2.0 G, and memory: 3.3 G
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpqo2dg63c/worker_log.txt
Got message from job at time 03-02-2020 18:12:44: Using the following configuration:
<cactusWorkflowConfig distanceToAddToRootAlignment="0.1">
    <constants defaultCpu="1" defaultMemory="3500000000" defaultOverlargeCpu="1" defaultOverlargeMemory="3500000000">

        <divergences five="0.35" four="0.25" one="0.1" three="0.2" two="0.15" useDefault="0" />
    </constants>
    <preprocessor check="1" checkAssemblyHub="0" memory="2000000000" preprocessJob="checkUniqueHeaders" />
    <preprocessor chunkSize="3000000" lastzOpts="--step=3 --ambiguous=iupac,100,100 --ungapped --queryhsplimit=keep,nowarn:1500" memory="2000000000" minPeriod="50" preprocessJob="lastzRepeatMask" proportionToSample="0.2" unmask="0" />

    <trimBlast doTrimStrategy="1" keepParalogs="0" trimFlanking="10" trimMinSize="100" trimOutgroupDepth="1" trimOutgroupFlanking="2000" trimThreshold="1.0" trimWindowSize="1" />
    <ktserver memory="3500000000" />
    <setup makeEventHeadersAlphaNumeric="0" />

    <caf alignmentFilter="filterSecondariesByMultipleSpecies" alpha="0.001" annealingRounds="128" blockTrim="5" chunkSize="25000000" compressFiles="1" deannealingRounds="2 8" doPhylogeny="0" filterByIdentity="0" identityRatio="3" lastzDisk="mediumDisk" lastzMemory="2000000000" maxAdjacencyComponentSizeRatio="50" maxAlignmentsPerSite="5" maxRecoverableChainLength="500000" maxRecoverableChainsIterations="5" maximumMedianSequenceLengthBetweenLinkedEnds="1000" minLengthForChromosome="1000000" minimumBlockDegree="2" minimumBlockDegreeToCheckSupport="10" minimumBlockHomologySupport="0.05" minimumDistance="0.01" minimumIngroupDegree="1" minimumMapQValue="0.0" minimumNumberOfSpecies="1" minimumOutgroupDegree="0" minimumSequenceLengthForBlast="30" minimumTreeCoverage="0.0" numTreeBuildingThreads="2" overlapSize="10000" phylogenyBreakpointScalingFactor="1.0" phylogenyCostPerDupPerBase="0.00" phylogenyCostPerLossPerBase="0.02" phylogenyDistanceCorrectionMethod="jukesCantor" phylogenyDoSplitsWithSupportHigherThanThisAllAtOnce="0.44" phylogenyHomologyUnitType="chain" phylogenyKeepSingleDegreeBlocks="0" phylogenyMaxBaseDistance="100" phylogenyMaxBlockDistance="50" phylogenyNumTrees="30" phylogenyRootingMethod="bestRecon" phylogenyScoringMethod="reconCost" phylogenySkipSingleCopyBlocks="1" phylogenyTreeBuildingMethod="guidedNeighborJoining,splitDecomposition" proportionOfUnalignedBasesForNewChromosome="0.8" realign="1" realignArguments="--gapGamma 0.0 --matchGamma 0.9 --diagonalExpansion 4 --splitMatrixBiggerThanThis 10 --constraintDiagonalTrim 0 --alignAmbiguityCharacters --splitIndelsLongerThanThis 99" removeRecoverableChains="unequalNumberOfIngroupCopies" runMapQFiltering="1" trim="0 0">
        <divergence argName="lastzArguments" default="--step=1 --ambiguous=iupac,100,100 --ydrop=3000" five="--step=2 --ambiguous=iupac,100,100 --ydrop=3000" four="--step=3 --ambiguous=iupac,100,100 --ydrop=3000" one="--step=2 --ambiguous=iupac,100,100 --ydrop=3000 --notransition" three="--step=4 --ambiguous=iupac,100,100 --ydrop=3000" two="--step=5 --ambiguous=iupac,100,100 --ydrop=3000" />
        <CactusCafRecursion maxFlowerGroupSize="100000000" />
        <CactusCafWrapper maxFlowerGroupSize="25000000" minFlowerSize="1" />
        <CactusCafWrapperLarge2 overlargeMemory="5000000000" />
    </caf>

    <bar alignAmbiguityCharacters="1" anchorMatrixBiggerThanThis="500" bandingLimit="1000000" constraintDiagonalTrim="14" diagonalExpansion="20" gapGamma="0.0" largeEndSize="5000" matchGamma="0.2" minimumBlockDegree="2" minimumCoverageToRescue="0.5" minimumIngroupDegree="1" minimumNumberOfSpecies="1" minimumOutgroupDegree="0" minimumSizeToRescue="100" pruneOutStubAlignments="1" repeatMaskMatrixBiggerThanThis="500" rescue="0" runBar="1" spanningTrees="5" splitMatrixBiggerThanThis="3000" useBanding="1" useProgressiveMerging="1" veryLargeEndSize="2000000">
        <CactusBarRecursion maxFlowerGroupSize="100000000" />
        <CactusBarWrapper maxFlowerGroupSize="2000000" memory="2000000000" />
        <CactusBarWrapperLarge maxFlowerGroupSize="2000000" />
        <CactusBarEndAlignerWrapper memory="2000000000" />
    </bar>
    <normal iterations="2">
        <CactusNormalRecursion maxFlowerGroupSize="100000000" maxFlowerWrapperGroupSize="10000000" />
        <CactusNormalWrapper />
    </normal>
    <avg buildAvgs="0">
        <CactusAVGRecursion maxFlowerGroupSize="100000000" maxFlowerWrapperGroupSize="10000000" />
        <CactusAVGWrapper />
    </avg>
    <reference ignoreUnalignedGaps="1" makeScaffolds="1" matchingAlgorithm="blossom5" maxWalkForCalculatingZ="100000" minNumberOfSequencesToSupportAdjacency="1" numberOfNs="10" permutations="10" phi="1.0" reference="reference" theta="0.0001" useSimulatedAnnealing="1" wiggle="0.9999">
        <CactusReferenceRecursion maxFlowerGroupSize="100000000" maxFlowerWrapperGroupSize="2000000" />

        <CactusReferenceWrapper />

        <CactusSetReferenceCoordinatesUpWrapper />

        <CactusSetReferenceCoordinatesDownRecursion maxFlowerGroupSize="100000000" maxFlowerWrapperGroupSize="2000000" />

        <CactusSetReferenceCoordinatesDownWrapper />
    </reference>
    <check runCheck="1">
        <CactusCheckRecursion maxFlowerGroupSize="100000000" maxFlowerWrapperGroupSize="2000000" />
        <CactusCheckWrapper />
    </check>
    <hal buildFasta="1" buildHal="1">
        <CactusHalGeneratorRecursion maxFlowerGroupSize="2000000" />
        <CactusHalGeneratorUpWrapper />
    </hal>

    <multi_cactus>
        <outgroup ancestor_quality_fraction="0.75" max_num_outgroups="3" strategy="greedyPreference" threshold="0" />

        <decomposition default_internal_node_prefix="Anc" max_parallel_subtrees="50000" self_alignment="false" />

    </multi_cactus>

    <ProgressiveNext />

    <ProgressiveUp />

    <ProgressiveDown />

    <ProgressiveOut />

    <RunCactusPreprocessorThenProgressiveDown />

    <RunCactusPreprocessorThenProgressiveDown2 />

    <exportHal disk="2000000000" />
</cactusWorkflowConfig>
Got message from job at time 03-02-2020 18:12:44: input sequence IDs: {'simHuman_chr6': 'files/no-job/file-_n9bip8i/simHuman.chr6', 'simMouse_chr6': 'files/no-job/file-17am9v0l/simMouse.chr6', 'simRat_chr6': 'files/no-job/file-7otkd_8d/simRat.chr6', 'simCow_chr6': 'files/no-job/file-ez7085hn/simCow.chr6', 'simDog_chr6': 'files/no-job/file-zxbrrrcg/simDog.chr6'}
Got message from job at time 03-02-2020 18:12:44: Leaf names = ['simMouse_chr6', 'simRat_chr6', 'simCow_chr6', 'simDog_chr6', 'simHuman_chr6']
Job ended: 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instanced4_i1jqv
Issued job 'logAssemblyStats' kind-logAssemblyStats/instances7ujv97y with job batch system ID: 1 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'logAssemblyStats' kind-logAssemblyStats/instance68vrtwr_ with job batch system ID: 2 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'logAssemblyStats' kind-logAssemblyStats/instancedot5np4u with job batch system ID: 3 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'logAssemblyStats' kind-logAssemblyStats/instance_3o3gd_9 with job batch system ID: 4 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'logAssemblyStats' kind-logAssemblyStats/instanceim9s44il with job batch system ID: 5 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'CactusPreprocessor' kind-CactusPreprocessor/instanceyc8ozsyv with job batch system ID: 6 and cores: 1, disk: 1.6 G, and memory: 2.0 G
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpx5g7nwg4/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpuiz2upxi/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmprpu26xwp/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmps7zjik8p/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpsk1o2huy/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmps1vyeyfw/worker_log.txt
Job ended: 'CactusPreprocessor' kind-CactusPreprocessor/instanceyc8ozsyv
Issued job 'CactusPreprocessor2' kind-CactusPreprocessor2/instancerk5o30a1 with job batch system ID: 7 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'CactusPreprocessor2' kind-CactusPreprocessor2/instancejgbu1vsj with job batch system ID: 8 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'CactusPreprocessor2' kind-CactusPreprocessor2/instance8sazjecd with job batch system ID: 9 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'CactusPreprocessor2' kind-CactusPreprocessor2/instanceqlr__3ue with job batch system ID: 10 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'CactusPreprocessor2' kind-CactusPreprocessor2/instancebgb6vivn with job batch system ID: 11 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Job ended: 'logAssemblyStats' kind-logAssemblyStats/instanceim9s44il
The job seems to have left a log file, indicating failure: 'logAssemblyStats' kind-logAssemblyStats/instanceim9s44il
kind-logAssemblyStats/instanceim9s44il    INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
kind-logAssemblyStats/instanceim9s44il    INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
kind-logAssemblyStats/instanceim9s44il    WARNING:toil.resource:'JTRES_e4a44727b67279e3ffae431778bc008a' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
kind-logAssemblyStats/instanceim9s44il    WARNING:toil.resource:'JTRES_e4a44727b67279e3ffae431778bc008a' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
kind-logAssemblyStats/instanceim9s44il    INFO:cactus.shared.common:Running the command ['cactus_analyseAssembly', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmprpu26xwp/a2152ffa-c355-4175-8797-b185d353fa85/tmpkkr_chmm.tmp']
kind-logAssemblyStats/instanceim9s44il    cactus_analyseAssembly: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory
kind-logAssemblyStats/instanceim9s44il    Traceback (most recent call last):
kind-logAssemblyStats/instanceim9s44il      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/worker.py", line 366, in workerScript
kind-logAssemblyStats/instanceim9s44il        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
kind-logAssemblyStats/instanceim9s44il      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1392, in _runner
kind-logAssemblyStats/instanceim9s44il        returnValues = self._run(jobGraph, fileStore)
kind-logAssemblyStats/instanceim9s44il      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1329, in _run
kind-logAssemblyStats/instanceim9s44il        return self.run(fileStore)
kind-logAssemblyStats/instanceim9s44il      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1533, in run
kind-logAssemblyStats/instanceim9s44il        rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
kind-logAssemblyStats/instanceim9s44il      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 200, in logAssemblyStats
kind-logAssemblyStats/instanceim9s44il        analysisString = cactus_call(parameters=["cactus_analyseAssembly", sequenceFile], check_output=True)
kind-logAssemblyStats/instanceim9s44il      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/shared/common.py", line 1178, in cactus_call
kind-logAssemblyStats/instanceim9s44il        raise RuntimeError("Command %s failed with output: %s" % (call, output))
kind-logAssemblyStats/instanceim9s44il    RuntimeError: Command ['cactus_analyseAssembly', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmprpu26xwp/a2152ffa-c355-4175-8797-b185d353fa85/tmpkkr_chmm.tmp'] failed with output: 
kind-logAssemblyStats/instanceim9s44il    ERROR:toil.worker:Exiting the worker because of a failed job on host bp1-login01.data.bp.acrc.priv
kind-logAssemblyStats/instanceim9s44il    WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'logAssemblyStats' kind-logAssemblyStats/instanceim9s44il with ID kind-logAssemblyStats/instanceim9s44il to 5
Issued job 'logAssemblyStats' kind-logAssemblyStats/instanceim9s44il with job batch system ID: 12 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Job ended: 'logAssemblyStats' kind-logAssemblyStats/instances7ujv97y
.....
kind-PreprocessSequence/instancevcixswhb    INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
kind-PreprocessSequence/instancevcixswhb    INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
kind-PreprocessSequence/instancevcixswhb    WARNING:toil.resource:'JTRES_e4a44727b67279e3ffae431778bc008a' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
kind-PreprocessSequence/instancevcixswhb    INFO:toil.lib.bioio:Preparing sequence for preprocessing
kind-PreprocessSequence/instancevcixswhb    INFO:cactus.shared.common:Running the command ['cactus_blast_chunkSequences', 'INFO', '3000000', '0', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpj_ok6cp1/956b2326-1a1f-42e8-8efe-b5725e68457d/t7n71qxo3/tmp_BIb011sEAf', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpj_ok6cp1/956b2326-1a1f-42e8-8efe-b5725e68457d/tmpgctzoeac.tmp']
kind-PreprocessSequence/instancevcixswhb    cactus_blast_chunkSequences: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory
kind-PreprocessSequence/instancevcixswhb    Traceback (most recent call last):
kind-PreprocessSequence/instancevcixswhb      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/worker.py", line 366, in workerScript
kind-PreprocessSequence/instancevcixswhb        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
kind-PreprocessSequence/instancevcixswhb      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/shared/common.py", line 1239, in _runner
kind-PreprocessSequence/instancevcixswhb        super(RoundedJob, self)._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
kind-PreprocessSequence/instancevcixswhb      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1392, in _runner
kind-PreprocessSequence/instancevcixswhb        returnValues = self._run(jobGraph, fileStore)
kind-PreprocessSequence/instancevcixswhb      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1329, in _run
kind-PreprocessSequence/instancevcixswhb        return self.run(fileStore)
kind-PreprocessSequence/instancevcixswhb      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/preprocessor/cactus_preprocessor.py", line 139, in run
kind-PreprocessSequence/instancevcixswhb        overlapSize=0)
kind-PreprocessSequence/instancevcixswhb      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/shared/common.py", line 807, in runGetChunks
kind-PreprocessSequence/instancevcixswhb        chunksDir] + sequenceFiles)
kind-PreprocessSequence/instancevcixswhb      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/shared/common.py", line 1178, in cactus_call
kind-PreprocessSequence/instancevcixswhb        raise RuntimeError("Command %s failed with output: %s" % (call, output))
kind-PreprocessSequence/instancevcixswhb    RuntimeError: Command ['cactus_blast_chunkSequences', 'INFO', '3000000', '0', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpj_ok6cp1/956b2326-1a1f-42e8-8efe-b5725e68457d/t7n71qxo3/tmp_BIb011sEAf', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpj_ok6cp1/956b2326-1a1f-42e8-8efe-b5725e68457d/tmpgctzoeac.tmp'] failed with output: 
kind-PreprocessSequence/instancevcixswhb    ERROR:toil.worker:Exiting the worker because of a failed job on host bp1-login01.data.bp.acrc.priv
kind-PreprocessSequence/instancevcixswhb    WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'PreprocessSequence' kind-PreprocessSequence/instancevcixswhb with ID kind-PreprocessSequence/instancevcixswhb to 0
Job 'PreprocessSequence' kind-PreprocessSequence/instancevcixswhb with ID kind-PreprocessSequence/instancevcixswhb is completely failed
Finished toil run with 27 failed jobs.
Failed jobs at end of the run: 'logAssemblyStats' kind-logAssemblyStats/instancedot5np4u 'PreprocessSequence' kind-PreprocessSequence/instance597qlgy7 'BatchPreprocessor' kind-BatchPreprocessor/instanceervnz9x3 'BatchPreprocessor' kind-BatchPreprocessor/instance1djvjw3l 'PreprocessSequence' kind-PreprocessSequence/instancevcixswhb 'PreprocessSequence' kind-PreprocessSequence/instancefqvfiw6_ 'BatchPreprocessor' kind-BatchPreprocessor/instance1kezfy44 'logAssemblyStats' kind-logAssemblyStats/instance_3o3gd_9 'PreprocessSequence' kind-PreprocessSequence/instancemrp99dm6 'CactusPreprocessor2' kind-CactusPreprocessor2/instancerk5o30a1 'logAssemblyStats' kind-logAssemblyStats/instances7ujv97y 'PreprocessSequence' kind-PreprocessSequence/instance_ll97_rk 'BatchPreprocessor' kind-BatchPreprocessor/instance3ibd_x_3 'CactusPreprocessor' kind-CactusPreprocessor/instanceyc8ozsyv 'logAssemblyStats' kind-logAssemblyStats/instance68vrtwr_ 'BatchPreprocessor' kind-BatchPreprocessor/instance3lmzts3n 'CactusPreprocessor2' kind-CactusPreprocessor2/instance8sazjecd 'CactusPreprocessor2' kind-CactusPreprocessor2/instancejgbu1vsj 'BatchPreprocessor' kind-BatchPreprocessor/instance0_t15aw1 'logAssemblyStats' kind-logAssemblyStats/instanceim9s44il 'BatchPreprocessor' kind-BatchPreprocessor/instanceaf23clos 'BatchPreprocessor' kind-BatchPreprocessor/instancekl4t1648 'CactusPreprocessor2' kind-CactusPreprocessor2/instanceqlr__3ue 'CactusPreprocessor2' kind-CactusPreprocessor2/instancebgb6vivn 'BatchPreprocessor' kind-BatchPreprocessor/instancegxcbrtho 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instanced4_i1jqv 'BatchPreprocessor' kind-BatchPreprocessor/instancepzntxu8r
Traceback (most recent call last):
  File "cactus_env/bin/cactus", line 8, in <module>
    sys.exit(main())
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 474, in main
    runCactusProgressive(options)
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/cactus/progressive/cactus_progressive.py", line 524, in runCactusProgressive
    halID = toil.start(RunCactusPreprocessorThenProgressiveDown(options, project, memory=configWrapper.getDefaultMemory()))
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/common.py", line 800, in start
    return self._runMainLoop(rootJobGraph)
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/common.py", line 1070, in _runMainLoop
    jobCache=self._jobCache).run()
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/leader.py", line 246, in run
    raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
toil.leader.FailedJobsException

@diekhans can you help me? Thanks a lot F

diekhans commented 4 years ago

It looks like you compiled with phylop enabled (ENABLE_PHYLOP defined). You need to follow the instructions in

submodules/hal/README.md

to install the dependencies.

Francesco Cicconardi notifications@github.com writes:

Ok @diekhans,

I fix that issue, now I'm facing this problem:

h5c++  -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I../../clapack/INCLUDE -I../../clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -I tests -o ../bin/halHdf5Tests ../objs/api/hdf5_tests/hdf5SegmentTypeTest.o ../objs/api/hdf5_tests/hdf5ExternalArrayTest.o ../objs/api/hdf5_tests/allTests.o ../objs/api/hdf5_tests/hdf5SequenceTypeTest.o ../objs/api/hdf5_tests/hdf5DnaTypeTest.o ../objs/api/hdf5_tests/hdf5Test.o  ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a -L../../phast/lib -lphast -L../../clapack -L../../clapack/F2CLIBS -llapack -ltmg -lblaswr -lf2c 
/usr/bin/ld: cannot find -lphast
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -ltmg
/usr/bin/ld: cannot find -lblaswr
/usr/bin/ld: cannot find -lf2c

Are these other dependecies? Cheers F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-593468235 Ok @diekhans,

I fix that issue, now I'm facing this problem:

h5c++ -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I../../clapack/INCLUDE -I../../clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -Ihdf5_impl -Immap_impl -I tests -o ../bin/halHdf5Tests ../objs/api/hdf5_tests/hdf5SegmentTypeTest.o ../objs/api/hdf5_tests/hdf5ExternalArrayTest.o ../objs/api/hdf5_tests/allTests.o ../objs/api/hdf5_tests/hdf5SequenceTypeTest.o ../objs/api/hdf5_tests/hdf5DnaTypeTest.o ../objs/api/hdf5_tests/hdf5Test.o ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a -L../../phast/lib -lphast -L../../clapack -L../../clapack/F2CLIBS -llapack -ltmg -lblaswr -lf2c /usr/bin/ld: cannot find -lphast /usr/bin/ld: cannot find -llapack /usr/bin/ld: cannot find -ltmg /usr/bin/ld: cannot find -lblaswr /usr/bin/ld: cannot find -lf2c

Are these other dependecies? Cheers F

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

diekhans commented 4 years ago

The cactus command is created by doing the

pip install .

into your virtual environment

Francesco Cicconardi notifications@github.com writes:

it seems like it worked

make suball1
make[1]: Entering directory `/home/tk19812/software/cactus'
#cd submodules/kyoto && KT_OPTIONS=--disable-lua make PREFIX=/home/tk19812/software/cactus && make install
#cd submodules/sonLib && PKG_CONFIG_PATH=/home/tk19812/software/cactus/lib/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig make
#mkdir -p bin
#ln -f submodules/sonLib/bin/[a-zA-Z]* bin/
cd submodules/cPecan && make
make[2]: Entering directory `/home/tk19812/software/cactus/submodules/cPecan'
cd externalTools && make all
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools'
cd lastz-distrib-1.03.54 && make install
make[4]: Entering directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54'
cd src && make install
make[5]: Entering directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54/src'
install -d      ../../../../sonLib/bin
install lastz   ../../../../sonLib/bin
install lastz_D ../../../../sonLib/bin
make[5]: Leaving directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54/src'
make[4]: Leaving directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54'
mv /home/tk19812/software/cactus/submodules/sonLib/bin/lastz /home/tk19812/software/cactus/submodules/sonLib/bin/cPecanLastz
mv /home/tk19812/software/cactus/submodules/sonLib/bin/lastz_D /home/tk19812/software/cactus/submodules/sonLib/bin/cPecanLastz_D
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/cPecan/externalTools'
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/cPecan'
cd submodules/hal &&  make
make[2]: Entering directory `/home/tk19812/software/cactus/submodules/hal'
cd api && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/api'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/api'
cd stats && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/stats'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/stats'
cd randgen && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/randgen'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/randgen'
cd validate && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/validate'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/validate'
cd mutations && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/mutations'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/mutations'
cd fasta && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/fasta'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/fasta'
cd alignmentDepth && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
cd liftover && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/liftover'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/liftover'
cd lod && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/lod'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/lod'
cd maf && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/maf'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/maf'
cd blockViz && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
cd extract && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/extract'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/extract'
cd analysis && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/analysis'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/analysis'
cd phyloP && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
cd modify && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/modify'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/modify'
cd assemblyHub && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
cd synteny && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/synteny'
cd api && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/api'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/api'
cd stats && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/stats'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/stats'
cd randgen && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/randgen'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/randgen'
cd validate && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/validate'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/validate'
cd mutations && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/mutations'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/mutations'
cd fasta && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/fasta'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/fasta'
cd alignmentDepth && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
cd liftover && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/liftover'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/liftover'
cd lod && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/lod'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/lod'
cd maf && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/maf'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/maf'
cd blockViz && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
cd extract && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/extract'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/extract'
cd analysis && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/analysis'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/analysis'
cd phyloP && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
cd modify && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/modify'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/modify'
cd assemblyHub && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
cd synteny && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/hal'
mkdir -p bin
ln -f submodules/hal/bin/* bin/
ln -f submodules/hal/lib/libHal.a submodules/hal/lib/halLib.a
#cd submodules/matchingAndOrdering && make
#cd submodules/pinchesAndCacti && make
make[1]: Leaving directory `/home/tk19812/software/cactus'
make all_libs
make[1]: Entering directory `/home/tk19812/software/cactus'
make all_libs.api all_libs.setup all_libs.blastLib all_libs.caf all_libs.bar all_libs.blast all_libs.normalisation all_libs.hal all_libs.phylogeny all_libs.reference all_libs.faces all_libs.check all_libs.pipeline all_libs.preprocessor all_libs.hal all_libs.dbTest
make[2]: Entering directory `/home/tk19812/software/cactus'
cd api && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/api'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/api'
cd setup && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/setup'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/setup'
cd blastLib && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/blastLib'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blastLib'
cd caf && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/caf'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/caf'
cd bar && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/bar'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/bar'
cd blast && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/blast'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blast'
cd normalisation && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/normalisation'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/normalisation'
cd hal && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/hal'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/hal'
cd phylogeny && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/phylogeny'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/phylogeny'
cd reference && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/reference'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/reference'
cd faces && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/faces'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/faces'
cd check && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/check'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/check'
cd pipeline && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/pipeline'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/pipeline'
cd preprocessor && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/preprocessor'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/preprocessor'
make[2]: `all_libs.hal' is up to date.
cd dbTest && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/dbTest'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/dbTest'
make[2]: Leaving directory `/home/tk19812/software/cactus'
make[1]: Leaving directory `/home/tk19812/software/cactus'
make all_progs
make[1]: Entering directory `/home/tk19812/software/cactus'
make all_libs.api all_libs.setup all_libs.blastLib all_libs.caf all_libs.bar all_libs.blast all_libs.normalisation all_libs.hal all_libs.phylogeny all_libs.reference all_libs.faces all_libs.check all_libs.pipeline all_libs.preprocessor all_libs.hal all_libs.dbTest
make[2]: Entering directory `/home/tk19812/software/cactus'
cd api && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/api'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/api'
cd setup && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/setup'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/setup'
cd blastLib && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/blastLib'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blastLib'
cd caf && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/caf'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/caf'
cd bar && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/bar'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/bar'
cd blast && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/blast'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blast'
cd normalisation && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/normalisation'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/normalisation'
cd hal && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/hal'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/hal'
cd phylogeny && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/phylogeny'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/phylogeny'
cd reference && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/reference'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/reference'
cd faces && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/faces'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/faces'
cd check && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/check'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/check'
cd pipeline && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/pipeline'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/pipeline'
cd preprocessor && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/preprocessor'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/preprocessor'
make[2]: `all_libs.hal' is up to date.
cd dbTest && make all_libs
make[3]: Entering directory `/home/tk19812/software/cactus/dbTest'
make[3]: Nothing to be done for `all_libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/dbTest'
make[2]: Leaving directory `/home/tk19812/software/cactus'
make all_progs.api all_progs.setup all_progs.blastLib all_progs.caf all_progs.bar all_progs.blast all_progs.normalisation all_progs.hal all_progs.phylogeny all_progs.reference all_progs.faces all_progs.check all_progs.pipeline all_progs.preprocessor all_progs.hal all_progs.dbTest
make[2]: Entering directory `/home/tk19812/software/cactus'
cd api && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/api'
make ../bin//cactusAPITests 
make[4]: Entering directory `/home/tk19812/software/cactus/api'
make[4]: `../bin//cactusAPITests' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/api'
make[3]: Leaving directory `/home/tk19812/software/cactus/api'
cd setup && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/setup'
make ../bin//cactus_setup  
make[4]: Entering directory `/home/tk19812/software/cactus/setup'
make[4]: `../bin//cactus_setup' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/setup'
make[3]: Leaving directory `/home/tk19812/software/cactus/setup'
cd blastLib && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/blastLib'
make[3]: Nothing to be done for `all_progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/blastLib'
cd caf && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/caf'
make ../bin//stCafTests ../bin//cactus_caf
make[4]: Entering directory `/home/tk19812/software/cactus/caf'
make[4]: `../bin//stCafTests' is up to date.
make[4]: `../bin//cactus_caf' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/caf'
make[3]: Leaving directory `/home/tk19812/software/cactus/caf'
cd bar && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/bar'
make ../bin//cactus_bar ../bin//cactus_barTests
make[4]: Entering directory `/home/tk19812/software/cactus/bar'
make[4]: `../bin//cactus_bar' is up to date.
make[4]: `../bin//cactus_barTests' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/bar'
make[3]: Leaving directory `/home/tk19812/software/cactus/bar'
cd blast && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/blast'
make ../bin//cactus_convertAlignmentsToInternalNames ../bin//cactus_stripUniqueIDs ../bin//cactus_blast_convertCoordinates ../bin//cactus_blast_chunkSequences ../bin//cactus_blast_chunkFlowerSequences ../bin//cactus_blast_sortAlignments ../bin//cactus_calculateMappingQualities ../bin//cactus_mirrorAndOrientAlignments ../bin//cactus_splitAlignmentOverlaps ../bin//cactus_coverage
make[4]: Entering directory `/home/tk19812/software/cactus/blast'
make[4]: `../bin//cactus_convertAlignmentsToInternalNames' is up to date.
make[4]: `../bin//cactus_stripUniqueIDs' is up to date.
make[4]: `../bin//cactus_blast_convertCoordinates' is up to date.
make[4]: `../bin//cactus_blast_chunkSequences' is up to date.
make[4]: `../bin//cactus_blast_chunkFlowerSequences' is up to date.
make[4]: `../bin//cactus_blast_sortAlignments' is up to date.
make[4]: `../bin//cactus_calculateMappingQualities' is up to date.
make[4]: `../bin//cactus_mirrorAndOrientAlignments' is up to date.
make[4]: `../bin//cactus_splitAlignmentOverlaps' is up to date.
make[4]: `../bin//cactus_coverage' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/blast'
make[3]: Leaving directory `/home/tk19812/software/cactus/blast'
cd normalisation && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/normalisation'
make ../bin//cactus_normalisation
make[4]: Entering directory `/home/tk19812/software/cactus/normalisation'
make[4]: `../bin//cactus_normalisation' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/normalisation'
make[3]: Leaving directory `/home/tk19812/software/cactus/normalisation'
cd hal && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/hal'
make ../bin//cactus_halGenerator ../bin//cactus_halGeneratorTests ../bin//cactus_fastaGenerator
make[4]: Entering directory `/home/tk19812/software/cactus/hal'
make[4]: `../bin//cactus_halGenerator' is up to date.
make[4]: `../bin//cactus_halGeneratorTests' is up to date.
make[4]: `../bin//cactus_fastaGenerator' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/hal'
make[3]: Leaving directory `/home/tk19812/software/cactus/hal'
cd phylogeny && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/phylogeny'
make ../bin//cactus_phylogeny 
make[4]: Entering directory `/home/tk19812/software/cactus/phylogeny'
make[4]: `../bin//cactus_phylogeny' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/phylogeny'
make[3]: Leaving directory `/home/tk19812/software/cactus/phylogeny'
cd reference && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/reference'
make ../bin//cactus_reference ../bin//cactus_addReferenceCoordinates ../bin//referenceTests ../bin//cactus_getReferenceSeq
make[4]: Entering directory `/home/tk19812/software/cactus/reference'
make[4]: `../bin//cactus_reference' is up to date.
make[4]: `../bin//cactus_addReferenceCoordinates' is up to date.
make[4]: `../bin//referenceTests' is up to date.
make[4]: `../bin//cactus_getReferenceSeq' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/reference'
make[3]: Leaving directory `/home/tk19812/software/cactus/reference'
cd faces && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/faces'
make ../bin//cactus_fillAdjacencies
make[4]: Entering directory `/home/tk19812/software/cactus/faces'
make[4]: `../bin//cactus_fillAdjacencies' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/faces'
make[3]: Leaving directory `/home/tk19812/software/cactus/faces'
cd check && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/check'
make ../bin//cactus_check 
make[4]: Entering directory `/home/tk19812/software/cactus/check'
make[4]: `../bin//cactus_check' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/check'
make[3]: Leaving directory `/home/tk19812/software/cactus/check'
cd pipeline && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/pipeline'
make ../bin//cactus_workflow_getFlowers ../bin//cactus_workflow_extendFlowers ../bin//cactus_workflow_flowerStats ../bin//cactus_workflow_convertAlignmentCoordinates ../bin//cactus_secondaryDatabase ../bin//docker_test_script
make[4]: Entering directory `/home/tk19812/software/cactus/pipeline'
make[4]: `../bin//cactus_workflow_getFlowers' is up to date.
make[4]: `../bin//cactus_workflow_extendFlowers' is up to date.
make[4]: `../bin//cactus_workflow_flowerStats' is up to date.
make[4]: `../bin//cactus_workflow_convertAlignmentCoordinates' is up to date.
make[4]: `../bin//cactus_secondaryDatabase' is up to date.
make[4]: `../bin//docker_test_script' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/pipeline'
make[3]: Leaving directory `/home/tk19812/software/cactus/pipeline'
cd preprocessor && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/preprocessor'
make ../bin//cactus_analyseAssembly ../bin//cactus_batch_mergeChunks ../bin//cactus_makeAlphaNumericHeaders.py ../bin//cactus_filterSmallFastaSequences.py
make[4]: Entering directory `/home/tk19812/software/cactus/preprocessor'
make[4]: `../bin//cactus_analyseAssembly' is up to date.
make[4]: `../bin//cactus_batch_mergeChunks' is up to date.
make[4]: `../bin//cactus_makeAlphaNumericHeaders.py' is up to date.
make[4]: `../bin//cactus_filterSmallFastaSequences.py' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/preprocessor'
cd lastzRepeatMasking && make all
make[4]: Entering directory `/home/tk19812/software/cactus/preprocessor/lastzRepeatMasking'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/home/tk19812/software/cactus/preprocessor/lastzRepeatMasking'
make[3]: Leaving directory `/home/tk19812/software/cactus/preprocessor'
make[2]: `all_progs.hal' is up to date.
cd dbTest && make all_progs
make[3]: Entering directory `/home/tk19812/software/cactus/dbTest'
make ../bin//dbTestScript 
make[4]: Entering directory `/home/tk19812/software/cactus/dbTest'
make[4]: `../bin//dbTestScript' is up to date.
make[4]: Leaving directory `/home/tk19812/software/cactus/dbTest'
make[3]: Leaving directory `/home/tk19812/software/cactus/dbTest'
make[2]: Leaving directory `/home/tk19812/software/cactus'
make[1]: Leaving directory `/home/tk19812/software/cactus'
make suball2
make[1]: Entering directory `/home/tk19812/software/cactus'
#cd submodules/kyoto && KT_OPTIONS=--disable-lua make PREFIX=/home/tk19812/software/cactus && make install
#cd submodules/sonLib && PKG_CONFIG_PATH=/home/tk19812/software/cactus/lib/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig make
#mkdir -p bin
#ln -f submodules/sonLib/bin/[a-zA-Z]* bin/
cd submodules/hal &&  make
make[2]: Entering directory `/home/tk19812/software/cactus/submodules/hal'
cd api && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/api'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/api'
cd stats && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/stats'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/stats'
cd randgen && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/randgen'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/randgen'
cd validate && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/validate'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/validate'
cd mutations && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/mutations'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/mutations'
cd fasta && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/fasta'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/fasta'
cd alignmentDepth && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
cd liftover && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/liftover'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/liftover'
cd lod && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/lod'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/lod'
cd maf && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/maf'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/maf'
cd blockViz && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
cd extract && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/extract'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/extract'
cd analysis && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/analysis'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/analysis'
cd phyloP && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
cd modify && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/modify'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/modify'
cd assemblyHub && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
cd synteny && make libs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[3]: Nothing to be done for `libs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/synteny'
cd api && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/api'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/api'
cd stats && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/stats'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/stats'
cd randgen && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/randgen'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/randgen'
cd validate && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/validate'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/validate'
cd mutations && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/mutations'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/mutations'
cd fasta && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/fasta'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/fasta'
cd alignmentDepth && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/alignmentDepth'
cd liftover && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/liftover'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/liftover'
cd lod && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/lod'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/lod'
cd maf && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/maf'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/maf'
cd blockViz && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/blockViz'
cd extract && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/extract'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/extract'
cd analysis && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/analysis'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/analysis'
cd phyloP && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/phyloP'
cd modify && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/modify'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/modify'
cd assemblyHub && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/assemblyHub'
cd synteny && make progs
make[3]: Entering directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[3]: Nothing to be done for `progs'.
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/hal/synteny'
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/hal'
mkdir -p bin
ln -f submodules/hal/bin/* bin/
ln -f submodules/hal/lib/libHal.a submodules/hal/lib/halLib.a
cd api && make all_libs
make[2]: Entering directory `/home/tk19812/software/cactus/api'
make[2]: Nothing to be done for `all_libs'.
make[2]: Leaving directory `/home/tk19812/software/cactus/api'
cd submodules/cactus2hal && make
make[2]: Entering directory `/home/tk19812/software/cactus/submodules/cactus2hal'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/cactus2hal'
mkdir -p bin
ln -f submodules/cactus2hal/bin/* bin/
make[1]: Leaving directory `/home/tk19812/software/cactus'

but I can't see the cactus binary in the bin folder F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-593532819 it seems like it worked

make suball1 make[1]: Entering directory `/home/tk19812/software/cactus'

cd submodules/kyoto && KT_OPTIONS=--disable-lua make PREFIX=/home/tk19812/software/cactus && make install

cd submodules/sonLib && PKG_CONFIG_PATH=/home/tk19812/software/cactus/lib/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig make

mkdir -p bin

ln -f submodules/sonLib/bin/[a-zA-Z]* bin/

cd submodules/cPecan && make make[2]: Entering directory /home/tk19812/software/cactus/submodules/cPecan' cd externalTools && make all make[3]: Entering directory/home/tk19812/software/cactus/submodules/cPecan/externalTools' cd lastz-distrib-1.03.54 && make install make[4]: Entering directory /home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54' cd src && make install make[5]: Entering directory/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54/src' install -d ../../../../sonLib/bin install lastz ../../../../sonLib/bin install lastz_D ../../../../sonLib/bin make[5]: Leaving directory /home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54/src' make[4]: Leaving directory/home/tk19812/software/cactus/submodules/cPecan/externalTools/lastz-distrib-1.03.54' mv /home/tk19812/software/cactus/submodules/sonLib/bin/lastz /home/tk19812/software/cactus/submodules/sonLib/bin/cPecanLastz mv /home/tk19812/software/cactus/submodules/sonLib/bin/lastz_D /home/tk19812/software/cactus/submodules/sonLib/bin/cPecanLastz_D make[3]: Leaving directory /home/tk19812/software/cactus/submodules/cPecan/externalTools' make[2]: Leaving directory/home/tk19812/software/cactus/submodules/cPecan' cd submodules/hal && make make[2]: Entering directory /home/tk19812/software/cactus/submodules/hal' cd api && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/api' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/api' cd stats && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/stats' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/stats' cd randgen && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/randgen' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/randgen' cd validate && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/validate' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/validate' cd mutations && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/mutations' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/mutations' cd fasta && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/fasta' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/fasta' cd alignmentDepth && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/alignmentDepth' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/alignmentDepth' cd liftover && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/liftover' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/liftover' cd lod && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/lod' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/lod' cd maf && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/maf' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/maf' cd blockViz && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/blockViz' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/blockViz' cd extract && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/extract' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/extract' cd analysis && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/analysis' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/analysis' cd phyloP && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/phyloP' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/phyloP' cd modify && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/modify' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/modify' cd assemblyHub && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/assemblyHub' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/assemblyHub' cd synteny && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/synteny' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/synteny' cd api && make progs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/api' make[3]: Nothing to be done forprogs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/api' cd stats && make progs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/stats' make[3]: Nothing to be done for progs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/stats' cd randgen && make progs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/randgen' make[3]: Nothing to be done forprogs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/randgen' cd validate && make progs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/validate' make[3]: Nothing to be done for progs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/validate' cd mutations && make progs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/mutations' make[3]: Nothing to be done forprogs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/mutations' cd fasta && make progs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/fasta' make[3]: Nothing to be done for progs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/fasta' cd alignmentDepth && make progs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/alignmentDepth' make[3]: Nothing to be done forprogs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/alignmentDepth' cd liftover && make progs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/liftover' make[3]: Nothing to be done for progs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/liftover' cd lod && make progs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/lod' make[3]: Nothing to be done forprogs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/lod' cd maf && make progs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/maf' make[3]: Nothing to be done for progs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/maf' cd blockViz && make progs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/blockViz' make[3]: Nothing to be done forprogs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/blockViz' cd extract && make progs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/extract' make[3]: Nothing to be done for progs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/extract' cd analysis && make progs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/analysis' make[3]: Nothing to be done forprogs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/analysis' cd phyloP && make progs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/phyloP' make[3]: Nothing to be done for progs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/phyloP' cd modify && make progs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/modify' make[3]: Nothing to be done forprogs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/modify' cd assemblyHub && make progs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/assemblyHub' make[3]: Nothing to be done for progs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/assemblyHub' cd synteny && make progs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/synteny' make[3]: Nothing to be done forprogs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/synteny' make[2]: Leaving directory/home/tk19812/software/cactus/submodules/hal' mkdir -p bin ln -f submodules/hal/bin/* bin/ ln -f submodules/hal/lib/libHal.a submodules/hal/lib/halLib.a

cd submodules/matchingAndOrdering && make

cd submodules/pinchesAndCacti && make

make[1]: Leaving directory /home/tk19812/software/cactus' make all_libs make[1]: Entering directory/home/tk19812/software/cactus' make all_libs.api all_libs.setup all_libs.blastLib all_libs.caf all_libs.bar all_libs.blast all_libs.normalisation all_libs.hal all_libs.phylogeny all_libs.reference all_libs.faces all_libs.check all_libs.pipeline all_libs.preprocessor all_libs.hal all_libs.dbTest make[2]: Entering directory /home/tk19812/software/cactus' cd api && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/api' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/api' cd setup && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/setup' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/setup' cd blastLib && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/blastLib' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/blastLib' cd caf && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/caf' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/caf' cd bar && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/bar' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/bar' cd blast && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/blast' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/blast' cd normalisation && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/normalisation' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/normalisation' cd hal && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/hal' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/hal' cd phylogeny && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/phylogeny' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/phylogeny' cd reference && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/reference' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/reference' cd faces && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/faces' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/faces' cd check && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/check' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/check' cd pipeline && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/pipeline' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/pipeline' cd preprocessor && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/preprocessor' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/preprocessor' make[2]:all_libs.hal' is up to date. cd dbTest && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/dbTest' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/dbTest' make[2]: Leaving directory/home/tk19812/software/cactus' make[1]: Leaving directory /home/tk19812/software/cactus' make all_progs make[1]: Entering directory/home/tk19812/software/cactus' make all_libs.api all_libs.setup all_libs.blastLib all_libs.caf all_libs.bar all_libs.blast all_libs.normalisation all_libs.hal all_libs.phylogeny all_libs.reference all_libs.faces all_libs.check all_libs.pipeline all_libs.preprocessor all_libs.hal all_libs.dbTest make[2]: Entering directory /home/tk19812/software/cactus' cd api && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/api' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/api' cd setup && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/setup' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/setup' cd blastLib && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/blastLib' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/blastLib' cd caf && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/caf' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/caf' cd bar && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/bar' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/bar' cd blast && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/blast' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/blast' cd normalisation && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/normalisation' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/normalisation' cd hal && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/hal' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/hal' cd phylogeny && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/phylogeny' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/phylogeny' cd reference && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/reference' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/reference' cd faces && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/faces' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/faces' cd check && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/check' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/check' cd pipeline && make all_libs make[3]: Entering directory/home/tk19812/software/cactus/pipeline' make[3]: Nothing to be done for all_libs'. make[3]: Leaving directory/home/tk19812/software/cactus/pipeline' cd preprocessor && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/preprocessor' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/preprocessor' make[2]:all_libs.hal' is up to date. cd dbTest && make all_libs make[3]: Entering directory /home/tk19812/software/cactus/dbTest' make[3]: Nothing to be done forall_libs'. make[3]: Leaving directory /home/tk19812/software/cactus/dbTest' make[2]: Leaving directory/home/tk19812/software/cactus' make all_progs.api all_progs.setup all_progs.blastLib all_progs.caf all_progs.bar all_progs.blast all_progs.normalisation all_progs.hal all_progs.phylogeny all_progs.reference all_progs.faces all_progs.check all_progs.pipeline all_progs.preprocessor all_progs.hal all_progs.dbTest make[2]: Entering directory /home/tk19812/software/cactus' cd api && make all_progs make[3]: Entering directory/home/tk19812/software/cactus/api' make ../bin//cactusAPITests make[4]: Entering directory /home/tk19812/software/cactus/api' make[4]:../bin//cactusAPITests' is up to date. make[4]: Leaving directory /home/tk19812/software/cactus/api' make[3]: Leaving directory/home/tk19812/software/cactus/api' cd setup && make all_progs make[3]: Entering directory /home/tk19812/software/cactus/setup' make ../bin//cactus_setup make[4]: Entering directory/home/tk19812/software/cactus/setup' make[4]: ../bin//cactus_setup' is up to date. make[4]: Leaving directory/home/tk19812/software/cactus/setup' make[3]: Leaving directory /home/tk19812/software/cactus/setup' cd blastLib && make all_progs make[3]: Entering directory/home/tk19812/software/cactus/blastLib' make[3]: Nothing to be done for all_progs'. make[3]: Leaving directory/home/tk19812/software/cactus/blastLib' cd caf && make all_progs make[3]: Entering directory /home/tk19812/software/cactus/caf' make ../bin//stCafTests ../bin//cactus_caf make[4]: Entering directory/home/tk19812/software/cactus/caf' make[4]: ../bin//stCafTests' is up to date. make[4]:../bin//cactus_caf' is up to date. make[4]: Leaving directory /home/tk19812/software/cactus/caf' make[3]: Leaving directory/home/tk19812/software/cactus/caf' cd bar && make all_progs make[3]: Entering directory /home/tk19812/software/cactus/bar' make ../bin//cactus_bar ../bin//cactus_barTests make[4]: Entering directory/home/tk19812/software/cactus/bar' make[4]: ../bin//cactus_bar' is up to date. make[4]:../bin//cactus_barTests' is up to date. make[4]: Leaving directory /home/tk19812/software/cactus/bar' make[3]: Leaving directory/home/tk19812/software/cactus/bar' cd blast && make all_progs make[3]: Entering directory /home/tk19812/software/cactus/blast' make ../bin//cactus_convertAlignmentsToInternalNames ../bin//cactus_stripUniqueIDs ../bin//cactus_blast_convertCoordinates ../bin//cactus_blast_chunkSequences ../bin//cactus_blast_chunkFlowerSequences ../bin//cactus_blast_sortAlignments ../bin//cactus_calculateMappingQualities ../bin//cactus_mirrorAndOrientAlignments ../bin//cactus_splitAlignmentOverlaps ../bin//cactus_coverage make[4]: Entering directory/home/tk19812/software/cactus/blast' make[4]: ../bin//cactus_convertAlignmentsToInternalNames' is up to date. make[4]:../bin//cactus_stripUniqueIDs' is up to date. make[4]: ../bin//cactus_blast_convertCoordinates' is up to date. make[4]:../bin//cactus_blast_chunkSequences' is up to date. make[4]: ../bin//cactus_blast_chunkFlowerSequences' is up to date. make[4]:../bin//cactus_blast_sortAlignments' is up to date. make[4]: ../bin//cactus_calculateMappingQualities' is up to date. make[4]:../bin//cactus_mirrorAndOrientAlignments' is up to date. make[4]: ../bin//cactus_splitAlignmentOverlaps' is up to date. make[4]:../bin//cactus_coverage' is up to date. make[4]: Leaving directory /home/tk19812/software/cactus/blast' make[3]: Leaving directory/home/tk19812/software/cactus/blast' cd normalisation && make all_progs make[3]: Entering directory /home/tk19812/software/cactus/normalisation' make ../bin//cactus_normalisation make[4]: Entering directory/home/tk19812/software/cactus/normalisation' make[4]: ../bin//cactus_normalisation' is up to date. make[4]: Leaving directory/home/tk19812/software/cactus/normalisation' make[3]: Leaving directory /home/tk19812/software/cactus/normalisation' cd hal && make all_progs make[3]: Entering directory/home/tk19812/software/cactus/hal' make ../bin//cactus_halGenerator ../bin//cactus_halGeneratorTests ../bin//cactus_fastaGenerator make[4]: Entering directory /home/tk19812/software/cactus/hal' make[4]:../bin//cactus_halGenerator' is up to date. make[4]: ../bin//cactus_halGeneratorTests' is up to date. make[4]:../bin//cactus_fastaGenerator' is up to date. make[4]: Leaving directory /home/tk19812/software/cactus/hal' make[3]: Leaving directory/home/tk19812/software/cactus/hal' cd phylogeny && make all_progs make[3]: Entering directory /home/tk19812/software/cactus/phylogeny' make ../bin//cactus_phylogeny make[4]: Entering directory/home/tk19812/software/cactus/phylogeny' make[4]: ../bin//cactus_phylogeny' is up to date. make[4]: Leaving directory/home/tk19812/software/cactus/phylogeny' make[3]: Leaving directory /home/tk19812/software/cactus/phylogeny' cd reference && make all_progs make[3]: Entering directory/home/tk19812/software/cactus/reference' make ../bin//cactus_reference ../bin//cactus_addReferenceCoordinates ../bin//referenceTests ../bin//cactus_getReferenceSeq make[4]: Entering directory /home/tk19812/software/cactus/reference' make[4]:../bin//cactus_reference' is up to date. make[4]: ../bin//cactus_addReferenceCoordinates' is up to date. make[4]:../bin//referenceTests' is up to date. make[4]: ../bin//cactus_getReferenceSeq' is up to date. make[4]: Leaving directory/home/tk19812/software/cactus/reference' make[3]: Leaving directory /home/tk19812/software/cactus/reference' cd faces && make all_progs make[3]: Entering directory/home/tk19812/software/cactus/faces' make ../bin//cactus_fillAdjacencies make[4]: Entering directory /home/tk19812/software/cactus/faces' make[4]:../bin//cactus_fillAdjacencies' is up to date. make[4]: Leaving directory /home/tk19812/software/cactus/faces' make[3]: Leaving directory/home/tk19812/software/cactus/faces' cd check && make all_progs make[3]: Entering directory /home/tk19812/software/cactus/check' make ../bin//cactus_check make[4]: Entering directory/home/tk19812/software/cactus/check' make[4]: ../bin//cactus_check' is up to date. make[4]: Leaving directory/home/tk19812/software/cactus/check' make[3]: Leaving directory /home/tk19812/software/cactus/check' cd pipeline && make all_progs make[3]: Entering directory/home/tk19812/software/cactus/pipeline' make ../bin//cactus_workflow_getFlowers ../bin//cactus_workflow_extendFlowers ../bin//cactus_workflow_flowerStats ../bin//cactus_workflow_convertAlignmentCoordinates ../bin//cactus_secondaryDatabase ../bin//docker_test_script make[4]: Entering directory /home/tk19812/software/cactus/pipeline' make[4]:../bin//cactus_workflow_getFlowers' is up to date. make[4]: ../bin//cactus_workflow_extendFlowers' is up to date. make[4]:../bin//cactus_workflow_flowerStats' is up to date. make[4]: ../bin//cactus_workflow_convertAlignmentCoordinates' is up to date. make[4]:../bin//cactus_secondaryDatabase' is up to date. make[4]: ../bin//docker_test_script' is up to date. make[4]: Leaving directory/home/tk19812/software/cactus/pipeline' make[3]: Leaving directory /home/tk19812/software/cactus/pipeline' cd preprocessor && make all_progs make[3]: Entering directory/home/tk19812/software/cactus/preprocessor' make ../bin//cactus_analyseAssembly ../bin//cactus_batch_mergeChunks ../bin//cactus_makeAlphaNumericHeaders.py ../bin//cactus_filterSmallFastaSequences.py make[4]: Entering directory /home/tk19812/software/cactus/preprocessor' make[4]:../bin//cactus_analyseAssembly' is up to date. make[4]: ../bin//cactus_batch_mergeChunks' is up to date. make[4]:../bin//cactus_makeAlphaNumericHeaders.py' is up to date. make[4]: ../bin//cactus_filterSmallFastaSequences.py' is up to date. make[4]: Leaving directory/home/tk19812/software/cactus/preprocessor' cd lastzRepeatMasking && make all make[4]: Entering directory /home/tk19812/software/cactus/preprocessor/lastzRepeatMasking' make[4]: Nothing to be done forall'. make[4]: Leaving directory /home/tk19812/software/cactus/preprocessor/lastzRepeatMasking' make[3]: Leaving directory/home/tk19812/software/cactus/preprocessor' make[2]: all_progs.hal' is up to date. cd dbTest && make all_progs make[3]: Entering directory/home/tk19812/software/cactus/dbTest' make ../bin//dbTestScript make[4]: Entering directory /home/tk19812/software/cactus/dbTest' make[4]:../bin//dbTestScript' is up to date. make[4]: Leaving directory /home/tk19812/software/cactus/dbTest' make[3]: Leaving directory/home/tk19812/software/cactus/dbTest' make[2]: Leaving directory /home/tk19812/software/cactus' make[1]: Leaving directory/home/tk19812/software/cactus' make suball2 make[1]: Entering directory `/home/tk19812/software/cactus'

cd submodules/kyoto && KT_OPTIONS=--disable-lua make PREFIX=/home/tk19812/software/cactus && make install

cd submodules/sonLib && PKG_CONFIG_PATH=/home/tk19812/software/cactus/lib/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/bin/pkgconfig:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/bin/pkgconfig make

mkdir -p bin

ln -f submodules/sonLib/bin/[a-zA-Z]* bin/

cd submodules/hal && make make[2]: Entering directory /home/tk19812/software/cactus/submodules/hal' cd api && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/api' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/api' cd stats && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/stats' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/stats' cd randgen && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/randgen' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/randgen' cd validate && make libs make[3]: Entering directory /home/tk19812/software/cactus/submodules/hal/validate' make[3]: Nothing to be done forlibs'. make[3]: Leaving directory /home/tk19812/software/cactus/submodules/hal/validate' cd mutations && make libs make[3]: Entering directory/home/tk19812/software/cactus/submodules/hal/mutations' make[3]: Nothing to be done for libs'. make[3]: Leaving directory/home/tk19812/software/cactus/submodules/hal/mutations' cd fasta && make libs

francicco commented 4 years ago

I did that:

(cactus_env) [tk19812@bp1-login01 cactus]$ pip install .
Processing /home/tk19812/software/cactus
Requirement already satisfied: toil>=3.24 in ./cactus_env/lib/python3.7/site-packages (from Cactus==1.0) (3.24.0)
Requirement already satisfied: decorator in ./cactus_env/lib/python3.7/site-packages (from Cactus==1.0) (4.4.1)
Requirement already satisfied: psutil in ./cactus_env/lib/python3.7/site-packages (from Cactus==1.0) (5.7.0)
Requirement already satisfied: networkx<3,>=2 in ./cactus_env/lib/python3.7/site-packages (from Cactus==1.0) (2.4)
Requirement already satisfied: cython in ./cactus_env/lib/python3.7/site-packages (from Cactus==1.0) (0.29.15)
Requirement already satisfied: pytest in ./cactus_env/lib/python3.7/site-packages (from Cactus==1.0) (5.3.5)
Requirement already satisfied: dill==0.2.7.1 in ./cactus_env/lib/python3.7/site-packages (from toil>=3.24->Cactus==1.0) (0.2.7.1)
Requirement already satisfied: sphinx==1.7.5 in ./cactus_env/lib/python3.7/site-packages (from toil>=3.24->Cactus==1.0) (1.7.5)
Requirement already satisfied: future in ./cactus_env/lib/python3.7/site-packages (from toil>=3.24->Cactus==1.0) (0.18.2)
Requirement already satisfied: requests<3,>=2 in ./cactus_env/lib/python3.7/site-packages (from toil>=3.24->Cactus==1.0) (2.23.0)
Requirement already satisfied: six>=1.10.0 in ./cactus_env/lib/python3.7/site-packages (from toil>=3.24->Cactus==1.0) (1.14.0)
Requirement already satisfied: python-dateutil in ./cactus_env/lib/python3.7/site-packages (from toil>=3.24->Cactus==1.0) (2.8.1)
Requirement already satisfied: addict<=2.2.0 in ./cactus_env/lib/python3.7/site-packages (from toil>=3.24->Cactus==1.0) (2.2.0)
Requirement already satisfied: pathlib2==2.3.2 in ./cactus_env/lib/python3.7/site-packages (from toil>=3.24->Cactus==1.0) (2.3.2)
Requirement already satisfied: docker==2.5.1 in ./cactus_env/lib/python3.7/site-packages (from toil>=3.24->Cactus==1.0) (2.5.1)
Requirement already satisfied: more-itertools>=4.0.0 in ./cactus_env/lib/python3.7/site-packages (from pytest->Cactus==1.0) (8.2.0)
Requirement already satisfied: wcwidth in ./cactus_env/lib/python3.7/site-packages (from pytest->Cactus==1.0) (0.1.8)
Requirement already satisfied: packaging in ./cactus_env/lib/python3.7/site-packages (from pytest->Cactus==1.0) (20.1)
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in ./cactus_env/lib/python3.7/site-packages (from pytest->Cactus==1.0) (1.5.0)
Requirement already satisfied: pluggy<1.0,>=0.12 in ./cactus_env/lib/python3.7/site-packages (from pytest->Cactus==1.0) (0.13.1)
Requirement already satisfied: attrs>=17.4.0 in ./cactus_env/lib/python3.7/site-packages (from pytest->Cactus==1.0) (19.3.0)
Requirement already satisfied: py>=1.5.0 in ./cactus_env/lib/python3.7/site-packages (from pytest->Cactus==1.0) (1.8.1)
Requirement already satisfied: docutils>=0.11 in ./cactus_env/lib/python3.7/site-packages (from sphinx==1.7.5->toil>=3.24->Cactus==1.0) (0.16)
Requirement already satisfied: Jinja2>=2.3 in ./cactus_env/lib/python3.7/site-packages (from sphinx==1.7.5->toil>=3.24->Cactus==1.0) (2.11.1)
Requirement already satisfied: Pygments>=2.0 in ./cactus_env/lib/python3.7/site-packages (from sphinx==1.7.5->toil>=3.24->Cactus==1.0) (2.5.2)
Requirement already satisfied: babel!=2.0,>=1.3 in ./cactus_env/lib/python3.7/site-packages (from sphinx==1.7.5->toil>=3.24->Cactus==1.0) (2.8.0)
Requirement already satisfied: imagesize in ./cactus_env/lib/python3.7/site-packages (from sphinx==1.7.5->toil>=3.24->Cactus==1.0) (1.2.0)
Requirement already satisfied: setuptools in ./cactus_env/lib/python3.7/site-packages (from sphinx==1.7.5->toil>=3.24->Cactus==1.0) (45.2.0)
Requirement already satisfied: sphinxcontrib-websupport in ./cactus_env/lib/python3.7/site-packages (from sphinx==1.7.5->toil>=3.24->Cactus==1.0) (1.2.0)
Requirement already satisfied: snowballstemmer>=1.1 in ./cactus_env/lib/python3.7/site-packages (from sphinx==1.7.5->toil>=3.24->Cactus==1.0) (2.0.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in ./cactus_env/lib/python3.7/site-packages (from sphinx==1.7.5->toil>=3.24->Cactus==1.0) (0.7.12)
Requirement already satisfied: certifi>=2017.4.17 in ./cactus_env/lib/python3.7/site-packages (from requests<3,>=2->toil>=3.24->Cactus==1.0) (2019.11.28)
Requirement already satisfied: chardet<4,>=3.0.2 in ./cactus_env/lib/python3.7/site-packages (from requests<3,>=2->toil>=3.24->Cactus==1.0) (3.0.4)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./cactus_env/lib/python3.7/site-packages (from requests<3,>=2->toil>=3.24->Cactus==1.0) (1.25.8)
Requirement already satisfied: idna<3,>=2.5 in ./cactus_env/lib/python3.7/site-packages (from requests<3,>=2->toil>=3.24->Cactus==1.0) (2.9)
Requirement already satisfied: websocket-client>=0.32.0 in ./cactus_env/lib/python3.7/site-packages (from docker==2.5.1->toil>=3.24->Cactus==1.0) (0.57.0)
Requirement already satisfied: docker-pycreds>=0.2.1 in ./cactus_env/lib/python3.7/site-packages (from docker==2.5.1->toil>=3.24->Cactus==1.0) (0.4.0)
Requirement already satisfied: pyparsing>=2.0.2 in ./cactus_env/lib/python3.7/site-packages (from packaging->pytest->Cactus==1.0) (2.4.6)
Requirement already satisfied: zipp>=0.5 in ./cactus_env/lib/python3.7/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pytest->Cactus==1.0) (3.0.0)
Requirement already satisfied: MarkupSafe>=0.23 in ./cactus_env/lib/python3.7/site-packages (from Jinja2>=2.3->sphinx==1.7.5->toil>=3.24->Cactus==1.0) (1.1.1)
Requirement already satisfied: pytz>=2015.7 in ./cactus_env/lib/python3.7/site-packages (from babel!=2.0,>=1.3->sphinx==1.7.5->toil>=3.24->Cactus==1.0) (2019.3)
Building wheels for collected packages: Cactus
  Building wheel for Cactus (setup.py) ... done
  Created wheel for Cactus: filename=Cactus-1.0-py3-none-any.whl size=148256 sha256=94a4743fd4750df704df97edccdb2e87be0a1ff646c3cfea9078f6c9688cb352
  Stored in directory: /tmp/pip-ephem-wheel-cache-xdysul89/wheels/1c/23/ae/729b1047180c10139e08094314fc8d567f043e921f7e139f8e
Successfully built Cactus
Installing collected packages: Cactus
  Attempting uninstall: Cactus
    Found existing installation: Cactus 1.0
    Uninstalling Cactus-1.0:
      Successfully uninstalled Cactus-1.0
Successfully installed Cactus-1.0

But the cactus binary is not in bin folder

-rwx------. 2 tk19812 bisc  19M Mar  2 17:32 ancestorsML
-r-x------. 2 tk19812 bisc 5.9K Mar  2 17:32 ancestorsMLMP.py
-rwx------. 2 tk19812 bisc  22M Mar  2 17:28 blockVizBed
-rwx------. 2 tk19812 bisc  22M Mar  2 17:28 blockVizMaf
-rwx------. 2 tk19812 bisc  22M Mar  2 17:28 blockVizTest
-rwx------. 2 tk19812 bisc 752K Feb 28 09:46 blossom5
-rwx------. 2 tk19812 bisc 2.0K Feb 28 09:46 blossom_randGraph.py
-rwx------. 2 tk19812 bisc 5.5K Mar  2 17:51 cactus2hal.py
-rwx------. 2 tk19812 bisc 1.6K Feb 27 09:45 cactus2hal-stitch.sh
-rwx------. 1 tk19812 bisc 3.4M Mar  2 17:50 cactus_addReferenceCoordinates
-rwx------. 1 tk19812 bisc 654K Mar  2 17:51 cactus_analyseAssembly
-rwx------. 1 tk19812 bisc 3.5M Mar  2 17:34 cactusAPITests
-rwx------. 1 tk19812 bisc 4.2M Mar  2 18:17 cactus_bar
-rwx------. 1 tk19812 bisc 4.0M Mar  2 18:17 cactus_barTests
-rwx------. 1 tk19812 bisc 629K Mar  2 17:51 cactus_batch_mergeChunks
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_blast_chunkFlowerSequences
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_blast_chunkSequences
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_blast_convertCoordinates
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_blast_sortAlignments
-rwx------. 1 tk19812 bisc 4.2M Mar  2 18:17 cactus_caf
-rwx------. 1 tk19812 bisc 635K Mar  2 17:50 cactus_calculateMappingQualities
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:51 cactus_check
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_convertAlignmentsToInternalNames
-rwx------. 1 tk19812 bisc 649K Mar  2 17:50 cactus_coverage
-rwx------. 1 tk19812 bisc  79K Mar  2 17:51 cactus_covered_intervals
-rwx------. 1 tk19812 bisc 5.3K Mar  2 17:51 cactus_fasta_fragments.py
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_fastaGenerator
-rwx------. 1 tk19812 bisc 5.4K Mar  2 17:51 cactus_fasta_softmask_intervals.py
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_fillAdjacencies
-rwx------. 1 tk19812 bisc 3.2K Mar  2 17:51 cactus_filterSmallFastaSequences.py
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_getReferenceSeq
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_halGenerator
-rwx------. 1 tk19812 bisc 3.1M Mar  2 17:50 cactus_halGeneratorTests
-rwx------. 1 tk19812 bisc 1.2K Mar  2 17:51 cactus_makeAlphaNumericHeaders.py
-rwx------. 1 tk19812 bisc 635K Mar  2 17:50 cactus_mirrorAndOrientAlignments
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_normalisation
-rwx------. 1 tk19812 bisc 3.7M Mar  2 17:50 cactus_phylogeny
-rwx------. 1 tk19812 bisc 3.4M Mar  2 17:50 cactus_reference
-rwx------. 1 tk19812 bisc 1.9M Mar  2 17:51 cactus_secondaryDatabase
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:34 cactus_setup
-rwx------. 1 tk19812 bisc 640K Mar  2 17:50 cactus_splitAlignmentOverlaps
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:50 cactus_stripUniqueIDs
-rwx------. 1 tk19812 bisc 3.0M Mar  2 17:51 cactus_workflow_convertAlignmentCoordinates
-rwx------. 1 tk19812 bisc 2.9M Mar  2 17:51 cactus_workflow_extendFlowers
-rwx------. 1 tk19812 bisc 2.9M Mar  2 17:51 cactus_workflow_flowerStats
-rwx------. 1 tk19812 bisc 2.9M Mar  2 17:51 cactus_workflow_getFlowers
-rwx------. 2 tk19812 bisc 1.2M Feb 28 09:46 cPecanAlign
-rwx------. 2 tk19812 bisc  24K Feb 28 09:46 cPecanEm
-rwxr-xr-x. 2 tk19812 bisc 519K Mar  2 18:16 cPecanLastz
-rwxr-xr-x. 2 tk19812 bisc 523K Mar  2 18:16 cPecanLastz_D
-rwx------. 2 tk19812 bisc 2.2M Feb 28 09:46 cPecanLibTests
-rwx------. 2 tk19812 bisc 3.9K Feb 28 09:46 cPecanModifyHmm
-rwx------. 2 tk19812 bisc 1.3M Feb 28 09:46 cPecanRealign
-rwx------. 1 tk19812 bisc 2.0M Mar  2 17:51 dbTestScript
-rwx------. 1 tk19812 bisc  158 Mar  2 17:51 docker_test_script
-rwx------. 2 tk19812 bisc  18M Mar  2 17:31 findRegionsExclusivelyInGroup
-r-x------. 2 tk19812 bisc  19K Mar  2 17:32 hal2assemblyHub.py
-rwx------. 2 tk19812 bisc  18M Mar  2 17:27 hal2fasta
-rwx------. 2 tk19812 bisc  20M Mar  2 17:28 hal2maf
-r-x------. 2 tk19812 bisc  15K Mar  2 17:28 hal2mafMP.py
-rwx------. 2 tk19812 bisc  24M Mar  2 17:33 hal2synteny
-rwx------. 2 tk19812 bisc  19M Mar  2 17:29 hal4dExtract
-rwx------. 2 tk19812 bisc  19M Mar  2 17:29 hal4dExtractTest
-rwx------. 2 tk19812 bisc  18M Mar  2 17:30 halAddToBranch
-rwx------. 2 tk19812 bisc  18M Mar  2 17:29 halAlignedExtract
-rwx------. 2 tk19812 bisc  18M Mar  2 17:27 halAlignmentDepth
-rwx------. 2 tk19812 bisc  18M Mar  2 17:19 halAlignmentTreesTest
-rwx------. 2 tk19812 bisc  19M Mar  2 17:51 halAppendCactusSubtree
-rwx------. 2 tk19812 bisc  18M Mar  2 17:30 halAppendSubtree
-rwx------. 2 tk19812 bisc  19M Mar  2 17:19 halBottomSegmentTest
-rwx------. 2 tk19812 bisc  18M Mar  2 17:26 halBranchMutations
-rwx------. 2 tk19812 bisc  20M Mar  2 17:20 halColumnIteratorTest
-rwx------. 2 tk19812 bisc  19M Mar  2 17:25 halCoverage
-rwx------. 2 tk19812 bisc  18M Mar  2 17:28 halExtract
-rwx------. 2 tk19812 bisc  19M Mar  2 17:20 halGappedSegmentIteratorTest
-rwx------. 2 tk19812 bisc  20M Mar  2 17:20 halGenomeTest
-rwx------. 2 tk19812 bisc  12M Mar  2 17:19 halHdf5Tests
-rwx------. 2 tk19812 bisc  18M Mar  2 17:26 halIndels
-rwx------. 2 tk19812 bisc  21M Mar  2 17:27 halLiftover
-rwx------. 2 tk19812 bisc  22M Mar  2 17:27 halLiftoverTests
-rwx------. 2 tk19812 bisc  19M Mar  2 17:27 halLodExtract
-rwx------. 2 tk19812 bisc  18M Mar  2 17:28 halMafTests
-rwx------. 2 tk19812 bisc  21M Mar  2 17:21 halMappedSegmentTest
-rwx------. 2 tk19812 bisc  19M Mar  2 17:29 halMaskExtract
-rwx------. 2 tk19812 bisc  18M Mar  2 17:21 halMetaDataTest
-rwx------. 2 tk19812 bisc  19M Mar  2 17:25 halPctId
-rwx------. 2 tk19812 bisc  19M Mar  2 17:30 halPhyloP
-r-x------. 2 tk19812 bisc  13K Mar  2 17:30 halPhyloPMP.py
-r-x------. 2 tk19812 bisc  12K Mar  2 17:30 halPhyloPTrain.py
-rwx------. 2 tk19812 bisc  19M Mar  2 17:25 halRandGen
-rwx------. 2 tk19812 bisc  18M Mar  2 17:21 halRearrangementTest
-rwx------. 2 tk19812 bisc  17M Mar  2 17:30 halRemoveGenome
-rwx------. 2 tk19812 bisc  18M Mar  2 17:31 halRenameGenomes
-rwx------. 2 tk19812 bisc  18M Mar  2 17:31 halRenameSequences
-rwx------. 2 tk19812 bisc  18M Mar  2 17:30 halReplaceGenome
-rwx------. 2 tk19812 bisc  18M Mar  2 17:21 halSequenceTest
-rwx------. 2 tk19812 bisc  17M Mar  2 17:31 halSetMetadata
-rwx------. 2 tk19812 bisc  19M Mar  2 17:29 halSingleCopyRegionsExtract
-rwx------. 2 tk19812 bisc  18M Mar  2 17:26 halSnps
-rwx------. 2 tk19812 bisc  18M Mar  2 17:25 halStats
-rwx------. 2 tk19812 bisc  18M Mar  2 17:26 halSummarizeMutations
-rwx------. 2 tk19812 bisc  19M Mar  2 17:26 halTestGen
-rwx------. 2 tk19812 bisc  19M Mar  2 17:21 halTopSegmentTest
-r-x------. 2 tk19812 bisc 3.1K Mar  2 17:29 halTreeNIBackground.py
-r-x------. 2 tk19812 bisc 4.8K Mar  2 17:29 halTreeNIConservation.py
-r-x------. 2 tk19812 bisc 4.2K Mar  2 17:29 halTreeNITurnover.py
-r-x------. 2 tk19812 bisc 6.0K Mar  2 17:30 halTreePhyloP.py
-rwx------. 2 tk19812 bisc  17M Mar  2 17:31 halUpdateBranchLengths
-rwx------. 2 tk19812 bisc  18M Mar  2 17:26 halValidate
-rwx------. 2 tk19812 bisc  19M Mar  2 17:21 halValidateTest
-rwx------. 2 tk19812 bisc  21M Mar  2 17:27 halWiggleLiftover
-rwx------. 2 tk19812 bisc  17M Mar  2 17:31 halWriteNucleotides
-rwx------. 1 tk19812 bisc 209K Feb 27 13:21 kccachetest
-rwx------. 1 tk19812 bisc 192K Feb 27 13:21 kcdirmgr
-rwx------. 1 tk19812 bisc 236K Feb 27 13:21 kcdirtest
-rwx------. 1 tk19812 bisc 305K Feb 27 13:21 kcforestmgr
-rwx------. 1 tk19812 bisc 337K Feb 27 13:21 kcforesttest
-rwx------. 1 tk19812 bisc 301K Feb 27 13:21 kcgrasstest
-rwx------. 1 tk19812 bisc 233K Feb 27 13:21 kchashmgr
-rwx------. 1 tk19812 bisc 273K Feb 27 13:21 kchashtest
-rwx------. 1 tk19812 bisc  35K Feb 27 13:21 kclangctest
-rwx------. 1 tk19812 bisc 862K Feb 27 13:21 kcpolymgr
-rwx------. 1 tk19812 bisc 974K Feb 27 13:21 kcpolytest
-rwx------. 1 tk19812 bisc 303K Feb 27 13:21 kcprototest
-rwx------. 1 tk19812 bisc 185K Feb 27 13:21 kcstashtest
-rwx------. 1 tk19812 bisc 337K Feb 27 13:21 kctreemgr
-rwx------. 1 tk19812 bisc 377K Feb 27 13:21 kctreetest
-rwx------. 1 tk19812 bisc  39K Feb 27 13:21 kcutilmgr
-rwx------. 1 tk19812 bisc 178K Feb 27 13:21 kcutiltest
-rwx------. 1 tk19812 bisc 159K Feb 27 13:21 ktremotemgr
-rwx------. 1 tk19812 bisc 167K Feb 27 13:21 ktremotetest
-rwx------. 1 tk19812 bisc 994K Feb 27 13:21 ktserver
-rwx------. 1 tk19812 bisc 894K Feb 27 13:21 kttimedmgr
-rwx------. 1 tk19812 bisc 962K Feb 27 13:21 kttimedtest
-rwx------. 1 tk19812 bisc  92K Feb 27 13:21 ktutilmgr
-rwx------. 1 tk19812 bisc 112K Feb 27 13:21 ktutilserv
-rwx------. 1 tk19812 bisc  92K Feb 27 13:21 ktutiltest
-rwx------. 2 tk19812 bisc  20M Mar  2 17:28 maf2hal
-rwxrwxr-x. 2 tk19812 bisc 3.5K Feb 28 09:46 matchGraph.py
-rwx------. 2 tk19812 bisc 1.1M Feb 28 09:46 matchingAndOrderingTests
-rwxrwxr-x. 2 tk19812 bisc  40K Feb 28 09:46 mwmatching.py
-rwx------. 1 tk19812 bisc 3.5M Mar  2 17:50 referenceTests
-rwx------. 2 tk19812 bisc 626K Feb 28 09:45 sonLib_cigarTest
-rwx------. 2 tk19812 bisc 2.9K Mar  2 18:17 sonLib_daemonize.py
-rwx------. 2 tk19812 bisc 615K Feb 28 09:45 sonLib_fastaCTest
-rwx------. 2 tk19812 bisc 2.1M Feb 28 09:45 sonLib_kvDatabaseTest
-rwx------. 2 tk19812 bisc 2.0M Feb 28 09:45 sonLibTests
-rwx------. 1 tk19812 bisc 4.3M Mar  2 18:17 stCafTests
-rwx------. 2 tk19812 bisc 1.7M Mar  2 18:17 stPinchesAndCactiTests

What am I missing? F

diekhans commented 4 years ago

cactus is build in the virtualenv bin directory, not the cactus bin directory.

francicco commented 4 years ago

Yes @diekhans,

but it's not working:

(cactus_env) [tk19812@bp1-login01 bin]$ ./cactus ~/software/cactus/jobStore ~/software/cactus/examples/evolverMammals.txt ~/software/cactus/examples/evolverMammals.hal --root mr --binariesMode local --restart
Limiting maxCores to CPU count of system (48).
Limiting maxMemory to physically available memory (404143419392).
Limiting maxDisk to physically available disk (19226877952).
Job Dir: instanced4_i1jqv
Job Dir: instance2a262wmd
Job Dir: instances7ujv97y
Job Dir: instance68vrtwr_
Job Dir: instancedot5np4u
Job Dir: instance_3o3gd_9
Job Dir: instanceim9s44il
Job Dir: instanceyc8ozsyv
Job Dir: instancerk5o30a1
Job Dir: instancejgbu1vsj
Job Dir: instance8sazjecd
Job Dir: instanceqlr__3ue
Job Dir: instancebgb6vivn
Job Dir: instance0_t15aw1
Job Dir: instancepzntxu8r
Job Dir: instance1djvjw3l
Job Dir: instance3ibd_x_3
Job Dir: instance3lmzts3n
Job Dir: instancegxcbrtho
Job Dir: instanceaf23clos
Job Dir: instance1kezfy44
Job Dir: instancekl4t1648
Job Dir: instanceervnz9x3
Job Dir: instancemrp99dm6
Job Dir: instancefqvfiw6_
Job Dir: instance597qlgy7
Job Dir: instance_ll97_rk
Job Dir: instancevcixswhb
Repairing job: kind-PreprocessSequence/instance_ll97_rk
Repairing job: kind-PreprocessSequence/instance597qlgy7
Repairing job: kind-logAssemblyStats/instancedot5np4u
Repairing job: kind-logAssemblyStats/instanceim9s44il
Repairing job: kind-PreprocessSequence/instancefqvfiw6_
Repairing job: kind-PreprocessSequence/instancevcixswhb
Repairing job: kind-logAssemblyStats/instances7ujv97y
Repairing job: kind-logAssemblyStats/instance_3o3gd_9
Repairing job: kind-PreprocessSequence/instancemrp99dm6
Repairing job: kind-logAssemblyStats/instance68vrtwr_
Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
Issued job 'PreprocessSequence' kind-PreprocessSequence/instance597qlgy7 with job batch system ID: 0 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'logAssemblyStats' kind-logAssemblyStats/instances7ujv97y with job batch system ID: 1 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'PreprocessSequence' kind-PreprocessSequence/instancevcixswhb with job batch system ID: 2 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'PreprocessSequence' kind-PreprocessSequence/instance_ll97_rk with job batch system ID: 3 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'logAssemblyStats' kind-logAssemblyStats/instanceim9s44il with job batch system ID: 4 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'PreprocessSequence' kind-PreprocessSequence/instancemrp99dm6 with job batch system ID: 5 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'PreprocessSequence' kind-PreprocessSequence/instancefqvfiw6_ with job batch system ID: 6 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'logAssemblyStats' kind-logAssemblyStats/instancedot5np4u with job batch system ID: 7 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'logAssemblyStats' kind-logAssemblyStats/instance_3o3gd_9 with job batch system ID: 8 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Issued job 'logAssemblyStats' kind-logAssemblyStats/instance68vrtwr_ with job batch system ID: 9 and cores: 1, disk: 2.0 G, and memory: 2.0 G
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpqbjw1pwr/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmp8nvaoovm/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpp_g56r31/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpy5gb5bca/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmppn5v1k4s/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpv37927k3/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmps3n2dw3o/worker_log.txt
INFO:toil.worker:Redirecting logging to /tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpwn2c4plo/worker_log.txt
Job ended: 'PreprocessSequence' kind-PreprocessSequence/instance597qlgy7
The job seems to have left a log file, indicating failure: 'PreprocessSequence' kind-PreprocessSequence/instance597qlgy7
kind-PreprocessSequence/instance597qlgy7    INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
kind-PreprocessSequence/instance597qlgy7    INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
kind-PreprocessSequence/instance597qlgy7    WARNING:toil.resource:'JTRES_e4a44727b67279e3ffae431778bc008a' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
kind-PreprocessSequence/instance597qlgy7    INFO:toil.lib.bioio:Preparing sequence for preprocessing
kind-PreprocessSequence/instance597qlgy7    INFO:cactus.shared.common:Running the command ['cactus_blast_chunkSequences', 'INFO', '3000000', '0', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpqbjw1pwr/650241e3-297f-4357-aabe-44fc0c8610b8/tu3he1q35/tmp_4hrxscRb3H', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpqbjw1pwr/650241e3-297f-4357-aabe-44fc0c8610b8/tmpagw5_u01.tmp']
kind-PreprocessSequence/instance597qlgy7    cactus_blast_chunkSequences: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory
kind-PreprocessSequence/instance597qlgy7    Traceback (most recent call last):
kind-PreprocessSequence/instance597qlgy7      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/worker.py", line 366, in workerScript
kind-PreprocessSequence/instance597qlgy7        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
kind-PreprocessSequence/instance597qlgy7      File "/home/tk19812/software/cactus/src/cactus/shared/common.py", line 1239, in _runner
kind-PreprocessSequence/instance597qlgy7        super(RoundedJob, self)._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
kind-PreprocessSequence/instance597qlgy7      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1392, in _runner
kind-PreprocessSequence/instance597qlgy7        returnValues = self._run(jobGraph, fileStore)
kind-PreprocessSequence/instance597qlgy7      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1329, in _run
kind-PreprocessSequence/instance597qlgy7        return self.run(fileStore)
kind-PreprocessSequence/instance597qlgy7      File "/home/tk19812/software/cactus/src/cactus/preprocessor/cactus_preprocessor.py", line 139, in run
kind-PreprocessSequence/instance597qlgy7        overlapSize=0)
kind-PreprocessSequence/instance597qlgy7      File "/home/tk19812/software/cactus/src/cactus/shared/common.py", line 807, in runGetChunks
kind-PreprocessSequence/instance597qlgy7        chunksDir] + sequenceFiles)
kind-PreprocessSequence/instance597qlgy7      File "/home/tk19812/software/cactus/src/cactus/shared/common.py", line 1178, in cactus_call
kind-PreprocessSequence/instance597qlgy7        raise RuntimeError("Command %s failed with output: %s" % (call, output))
kind-PreprocessSequence/instance597qlgy7    RuntimeError: Command ['cactus_blast_chunkSequences', 'INFO', '3000000', '0', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpqbjw1pwr/650241e3-297f-4357-aabe-44fc0c8610b8/tu3he1q35/tmp_4hrxscRb3H', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpqbjw1pwr/650241e3-297f-4357-aabe-44fc0c8610b8/tmpagw5_u01.tmp'] failed with output: 
kind-PreprocessSequence/instance597qlgy7    ERROR:toil.worker:Exiting the worker because of a failed job on host bp1-login01.data.bp.acrc.priv
kind-PreprocessSequence/instance597qlgy7    WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'PreprocessSequence' kind-PreprocessSequence/instance597qlgy7 with ID kind-PreprocessSequence/instance597qlgy7 to 5
Issued job 'PreprocessSequence' kind-PreprocessSequence/instance597qlgy7 with job batch system ID: 10 and cores: 1, disk: 2.0 G, and memory: 2.0 G
Job ended: 'PreprocessSequence' kind-PreprocessSequence/instancevcixswhb
...
The job seems to have left a log file, indicating failure: 'logAssemblyStats' kind-logAssemblyStats/instance68vrtwr_
kind-logAssemblyStats/instance68vrtwr_    INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
kind-logAssemblyStats/instance68vrtwr_    INFO:toil:Running Toil version 3.24.0-de586251cb579bcb80eef435825cb3cedc202f52.
kind-logAssemblyStats/instance68vrtwr_    WARNING:toil.resource:'JTRES_e4a44727b67279e3ffae431778bc008a' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
kind-logAssemblyStats/instance68vrtwr_    WARNING:toil.resource:'JTRES_e4a44727b67279e3ffae431778bc008a' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
kind-logAssemblyStats/instance68vrtwr_    INFO:cactus.shared.common:Running the command ['cactus_analyseAssembly', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpicet8x0r/185ff237-c213-4b9b-ac06-12593be239ac/tmp2kcof_y7.tmp']
kind-logAssemblyStats/instance68vrtwr_    cactus_analyseAssembly: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory
kind-logAssemblyStats/instance68vrtwr_    Traceback (most recent call last):
kind-logAssemblyStats/instance68vrtwr_      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/worker.py", line 366, in workerScript
kind-logAssemblyStats/instance68vrtwr_        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
kind-logAssemblyStats/instance68vrtwr_      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1392, in _runner
kind-logAssemblyStats/instance68vrtwr_        returnValues = self._run(jobGraph, fileStore)
kind-logAssemblyStats/instance68vrtwr_      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1329, in _run
kind-logAssemblyStats/instance68vrtwr_        return self.run(fileStore)
kind-logAssemblyStats/instance68vrtwr_      File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/job.py", line 1533, in run
kind-logAssemblyStats/instance68vrtwr_        rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
kind-logAssemblyStats/instance68vrtwr_      File "/home/tk19812/software/cactus/src/cactus/progressive/cactus_progressive.py", line 200, in logAssemblyStats
kind-logAssemblyStats/instance68vrtwr_        analysisString = cactus_call(parameters=["cactus_analyseAssembly", sequenceFile], check_output=True)
kind-logAssemblyStats/instance68vrtwr_      File "/home/tk19812/software/cactus/src/cactus/shared/common.py", line 1178, in cactus_call
kind-logAssemblyStats/instance68vrtwr_        raise RuntimeError("Command %s failed with output: %s" % (call, output))
kind-logAssemblyStats/instance68vrtwr_    RuntimeError: Command ['cactus_analyseAssembly', '/tmp/toil-d8275035-ba0a-4aee-9a1c-dc49d41f48b6-81657330c30e4f38a6b8e3469f401cce/tmpicet8x0r/185ff237-c213-4b9b-ac06-12593be239ac/tmp2kcof_y7.tmp'] failed with output: 
kind-logAssemblyStats/instance68vrtwr_    ERROR:toil.worker:Exiting the worker because of a failed job on host bp1-login01.data.bp.acrc.priv
kind-logAssemblyStats/instance68vrtwr_    WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'logAssemblyStats' kind-logAssemblyStats/instance68vrtwr_ with ID kind-logAssemblyStats/instance68vrtwr_ to 0
Job 'logAssemblyStats' kind-logAssemblyStats/instance68vrtwr_ with ID kind-logAssemblyStats/instance68vrtwr_ is completely failed
Finished toil run with 27 failed jobs.
Failed jobs at end of the run: 'BatchPreprocessor' kind-BatchPreprocessor/instanceaf23clos 'BatchPreprocessor' kind-BatchPreprocessor/instance3ibd_x_3 'CactusPreprocessor2' kind-CactusPreprocessor2/instance8sazjecd 'BatchPreprocessor' kind-BatchPreprocessor/instanceervnz9x3 'PreprocessSequence' kind-PreprocessSequence/instance_ll97_rk 'PreprocessSequence' kind-PreprocessSequence/instance597qlgy7 'BatchPreprocessor' kind-BatchPreprocessor/instance3lmzts3n 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instanced4_i1jqv 'BatchPreprocessor' kind-BatchPreprocessor/instancepzntxu8r 'CactusPreprocessor2' kind-CactusPreprocessor2/instancerk5o30a1 'logAssemblyStats' kind-logAssemblyStats/instancedot5np4u 'BatchPreprocessor' kind-BatchPreprocessor/instance0_t15aw1 'BatchPreprocessor' kind-BatchPreprocessor/instance1kezfy44 'logAssemblyStats' kind-logAssemblyStats/instanceim9s44il 'BatchPreprocessor' kind-BatchPreprocessor/instancekl4t1648 'BatchPreprocessor' kind-BatchPreprocessor/instance1djvjw3l 'CactusPreprocessor2' kind-CactusPreprocessor2/instancejgbu1vsj 'PreprocessSequence' kind-PreprocessSequence/instancefqvfiw6_ 'CactusPreprocessor' kind-CactusPreprocessor/instanceyc8ozsyv 'BatchPreprocessor' kind-BatchPreprocessor/instancegxcbrtho 'CactusPreprocessor2' kind-CactusPreprocessor2/instancebgb6vivn 'PreprocessSequence' kind-PreprocessSequence/instancevcixswhb 'logAssemblyStats' kind-logAssemblyStats/instances7ujv97y 'logAssemblyStats' kind-logAssemblyStats/instance_3o3gd_9 'PreprocessSequence' kind-PreprocessSequence/instancemrp99dm6 'logAssemblyStats' kind-logAssemblyStats/instance68vrtwr_ 'CactusPreprocessor2' kind-CactusPreprocessor2/instanceqlr__3ue
Traceback (most recent call last):
  File "./cactus", line 11, in <module>
    load_entry_point('Cactus', 'console_scripts', 'cactus')()
  File "/home/tk19812/software/cactus/src/cactus/progressive/cactus_progressive.py", line 474, in main
    runCactusProgressive(options)
  File "/home/tk19812/software/cactus/src/cactus/progressive/cactus_progressive.py", line 484, in runCactusProgressive
    halID = toil.restart()
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/common.py", line 832, in restart
    return self._runMainLoop(rootJobGraph)
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/common.py", line 1070, in _runMainLoop
    jobCache=self._jobCache).run()
  File "/home/tk19812/software/cactus/cactus_env/lib/python3.7/site-packages/toil/leader.py", line 246, in run
    raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
toil.leader.FailedJobsException
francicco commented 4 years ago

I don't understand the error? F

diekhans commented 4 years ago

The problem is: cactus_blast_chunkSequences: error while loading shared libraries: libkyototycoon.so.2: cannot open shared object file: No such file or directory

There was a fix check into the tree last week to no build dynamic kyoto libraries. However, if you didn't start with a clean tree, it would link with the lib/.so files.

Please do a new checkout and follow the instructions in the README.md

francicco commented 4 years ago

Can you please tell me what command to execute? I'm not very familiar with using different branches? I'm so confused!!! F

francicco commented 4 years ago

The branch I'm using is bring-back-kyoto-submodule

git clone --single-branch --branch bring-back-kyoto-submodule https://github.com/ComparativeGenomicsToolkit/cactus.git

And libkyototycoon.so.2 is actually in ~/software/cactus/lib/libkyototycoon.so.2 and in ~/software/cactus/submodules/kyoto/kyototycoo/libkyototycoon.so.2

F

diekhans commented 4 years ago

This is all merged into master now, the static compile fix was not in the bring-back-kyoto-submodule branch.

Please checkout master.

Francesco Cicconardi notifications@github.com writes:

The branch I'm using is bring-back-kyoto-submodule

git clone --single-branch --branch bring-back-kyoto-submodule https://github.com/ComparativeGenomicsToolkit/cactus.git

And libkyototycoon.so.2 is actually in ~/software/cactus/lib/libkyototycoon.so.2 and in ~/software/cactus/submodules/kyoto/kyototycoo/libkyototycoon.so.2

F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-593985389 The branch I'm using is bring-back-kyoto-submodule

git clone --single-branch --branch bring-back-kyoto-submodule https:// github.com/ComparativeGenomicsToolkit/cactus.git

And libkyototycoon.so.2 is actually in ~/software/cactus/lib/ libkyototycoon.so.2 and in ~/software/cactus/submodules/kyoto/kyototycoo/ libkyototycoon.so.2

F

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

diekhans commented 4 years ago

I'm so confused!!!

A common git experience

francicco commented 4 years ago

git checkout -b master https://github.com/ComparativeGenomicsToolkit/cactus.git ????

diekhans commented 4 years ago

I would suggest just starting with a fresh clone; deleting previous one:

git clone https://github.com/ComparativeGenomicsToolkit/cactus.git

It is much easier to help with remote debugging there is no danger of old build stuff being left around

francicco commented 4 years ago

Geez! installing everything??? Can I move some of the submodules to the new folder? F

diekhans commented 4 years ago

You could do a git checkout master rhen a get pull

Then do a make clean and make

Parallel make does work. make -j 10

On Mar 3, 2020, at 10:01 AM, Francesco Cicconardi notifications@github.com wrote:

 Geez! installing everything??? Can I move some of the submodules to the new folder? F

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

francicco commented 4 years ago

Now pip install --upgrade toil[all] gives me a tons of errors! mainly for psutil

F

diekhans commented 4 years ago

If you are using python 3.7, you need to do:

CPPFLAGS='-DPYPY_VERSION' pip install toil[all]

francicco commented 4 years ago

With virtualEnv cannot install psutil without I can. Was this module present in the previous version? This is a nightmare! F

diekhans commented 4 years ago

psutil installed fine here a couple of days ago. Are you starting with a new virtualenv? not running inside of another virtualenv while building one?

This is all why I recommend starting over and going throw the steps carefully.

Francesco Cicconardi notifications@github.com writes:

With virtualEnv cannot install psutil without I can. Was this module present in the previous version? This is a nightmare! F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594005811 With virtualEnv cannot install psutil without I can. Was this module present in the previous version? This is a nightmare! F

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.*

francicco commented 4 years ago

It's the 3.6 and it's not working with that option as well. F

francicco commented 4 years ago

And can't install kyoto libs:

g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o kcutiltest kcutiltest.o -L. -L/home/tk19812/software/cactus/lib -L/usr/local/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/libfabric/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib/release:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mpi/mic/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2018-u3/debugger_2018/iga/lib:/sw/lang/intel-psxe-2018-u3/debugger_2018/libipt/intel64/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/libfabric/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib/release:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/debugger_2019/libipt/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/sw/lib/hdf5-1.10.6/lib:/sw/lang/gcc-9.1.0/lib64:/sw/lang/gcc-9.1.0/lib:/home/tk19812/software/lua-5.3.5/lib:/home/tk19812/software/lzo-2.10/include -Wl,--as-needed  -lkyotocabinet -lz -lstdc++ -lrt -lpthread -lm -lc 
./libkyotocabinet.a(kccompress.o): In function `kyotocabinet::LZO::compress(void const*, unsigned long, unsigned long*, kyotocabinet::LZO::Mode)':
kccompress.cc:(.text+0x323): undefined reference to `lzo1x_1_compress'
kccompress.cc:(.text+0x35e): undefined reference to `lzo_crc32'
./libkyotocabinet.a(kccompress.o): In function `kyotocabinet::LZO::decompress(void const*, unsigned long, unsigned long*, kyotocabinet::LZO::Mode)':
kccompress.cc:(.text+0x431): undefined reference to `lzo1x_decompress_safe'
kccompress.cc:(.text+0x47a): undefined reference to `lzo1x_decompress'
kccompress.cc:(.text+0x4fc): undefined reference to `lzo_crc32'
./libkyotocabinet.a(kccompress.o): In function `kyotocabinet::LZO::calculate_crc(void const*, unsigned long, unsigned int)':
kccompress.cc:(.text+0x51c): undefined reference to `lzo_crc32'
./libkyotocabinet.a(kccompress.o): In function `_GLOBAL__sub_I_kccompress.cc':
kccompress.cc:(.text.startup+0x56): undefined reference to `__lzo_init_v2'
collect2: error: ld returned 1 exit status
make[3]: *** [kcutiltest] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/kyoto/kyotocabinet'
make[2]: *** [cabinet] Error 2
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/kyoto'
make[1]: *** [suball.kyoto] Error 2
make[1]: Leaving directory `/home/tk19812/software/cactus'
make: *** [all] Error 2

F

diekhans commented 4 years ago

You need to have lzo libraries installed on your system. It should be available in whatever package manager your linux flavor uses.

Francesco Cicconardi notifications@github.com writes:

And can't install kyoto libs:

g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o kcutiltest kcutiltest.o -L. -L/home/tk19812/software/cactus/lib -L/usr/local/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/libfabric/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib/release:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mpi/mic/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2018-u3/debugger_2018/iga/lib:/sw/lang/intel-psxe-2018-u3/debugger_2018/libipt/intel64/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/libfabric/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib/release:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/debugger_2019/libipt/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/sw/lib/hdf5-1.10.6/lib:/sw/lang/gcc-9.1.0/lib64:/sw/lang/gcc-9.1.0/lib:/home/tk19812/software/lua-5.3.5/lib:/home/tk19812/software/lzo-2.10/include -Wl,--as-needed  -lkyotocabinet -lz -lstdc++ -lrt -lpthread -lm -lc 
./libkyotocabinet.a(kccompress.o): In function `kyotocabinet::LZO::compress(void const*, unsigned long, unsigned long*, kyotocabinet::LZO::Mode)':
kccompress.cc:(.text+0x323): undefined reference to `lzo1x_1_compress'
kccompress.cc:(.text+0x35e): undefined reference to `lzo_crc32'
./libkyotocabinet.a(kccompress.o): In function `kyotocabinet::LZO::decompress(void const*, unsigned long, unsigned long*, kyotocabinet::LZO::Mode)':
kccompress.cc:(.text+0x431): undefined reference to `lzo1x_decompress_safe'
kccompress.cc:(.text+0x47a): undefined reference to `lzo1x_decompress'
kccompress.cc:(.text+0x4fc): undefined reference to `lzo_crc32'
./libkyotocabinet.a(kccompress.o): In function `kyotocabinet::LZO::calculate_crc(void const*, unsigned long, unsigned int)':
kccompress.cc:(.text+0x51c): undefined reference to `lzo_crc32'
./libkyotocabinet.a(kccompress.o): In function `_GLOBAL__sub_I_kccompress.cc':
kccompress.cc:(.text.startup+0x56): undefined reference to `__lzo_init_v2'
collect2: error: ld returned 1 exit status
make[3]: *** [kcutiltest] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory `/home/tk19812/software/cactus/submodules/kyoto/kyotocabinet'
make[2]: *** [cabinet] Error 2
make[2]: Leaving directory `/home/tk19812/software/cactus/submodules/kyoto'
make[1]: *** [suball.kyoto] Error 2
make[1]: Leaving directory `/home/tk19812/software/cactus'
make: *** [all] Error 2

F

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594066956And can't install kyoto libs:

g++ -g -O2 -Wall -fPIC -fsigned-char -g0 -O2 -Wno-unused-but-set-variable -Wno-unused-but-set-parameter -o kcutiltest kcutiltest.o -L. -L/home/tk19812/software/cactus/lib -L/usr/local/lib -Wl,-rpath-link,.:/usr/local/lib:.:/usr/local/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/libfabric/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib/release:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mpi/mic/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2018-u3/debugger_2018/iga/lib:/sw/lang/intel-psxe-2018-u3/debugger_2018/libipt/intel64/lib:/sw/lang/intel-psxe-2018-u3/compilers_and_libraries_2018.3.222/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/libfabric/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib/release:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mpi/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/ipp/lib/intel64:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/tbb/lib/intel64/gcc4.7:/sw/lang/intel-psxe-2019-u3/debugger_2019/libipt/intel64/lib:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/lib/intel64_lin:/sw/lang/intel-psxe-2019-u3/compilers_and_libraries_2019.3.199/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/sw/lib/hdf5-1.10.6/lib:/sw/lang/gcc-9.1.0/lib64:/sw/lang/gcc-9.1.0/lib:/home/tk19812/software/lua-5.3.5/lib:/home/tk19812/software/lzo-2.10/include -Wl,--as-needed -lkyotocabinet -lz -lstdc++ -lrt -lpthread -lm -lc ./libkyotocabinet.a(kccompress.o): In function kyotocabinet::LZO::compress(void const*, unsigned long, unsigned long*, kyotocabinet::LZO::Mode)': kccompress.cc:(.text+0x323): undefined reference tolzo1x_1_compress' kccompress.cc:(.text+0x35e): undefined reference to lzo_crc32' ./libkyotocabinet.a(kccompress.o): In functionkyotocabinet::LZO::decompress(void const, unsigned long, unsigned long, kyotocabinet::LZO::Mode)': kccompress.cc:(.text+0x431): undefined reference to lzo1x_decompress_safe' kccompress.cc:(.text+0x47a): undefined reference tolzo1x_decompress' kccompress.cc:(.text+0x4fc): undefined reference to lzo_crc32' ./libkyotocabinet.a(kccompress.o): In functionkyotocabinet::LZO::calculate_crc(void const*, unsigned long, unsigned int)': kccompress.cc:(.text+0x51c): undefined reference to lzo_crc32' ./libkyotocabinet.a(kccompress.o): In function_GLOBALsub_I_kccompress.cc': kccompress.cc:(.text.startup+0x56): undefined reference to `lzo_init_v2' collect2: error: ld returned 1 exit status make[3]: [kcutiltest] Error 1 make[3]: Waiting for unfinished jobs.... make[3]: Leaving directory /home/tk19812/software/cactus/submodules/kyoto/kyotocabinet' make[2]: *** [cabinet] Error 2 make[2]: Leaving directory/home/tk19812/software/cactus/submodules/kyoto' make[1]: [suball.kyoto] Error 2 make[1]: Leaving directory `/home/tk19812/software/cactus' make: [all] Error 2

F

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francicco commented 4 years ago

I have them /home/tk19812/software/lzo-2.10/include

francicco commented 4 years ago

this is how I installed them:

cd ~/software && wget http://www.oberhumer.com/opensource/lzo/download/lzo-2.10.tar.gz
tar xvf lzo-2.10.tar.gz
cd lzo-2.10 && ./configure --prefix ~/software/lzo-2.10 && make -j 28 && make check && make test && make install && cd ..
diekhans commented 4 years ago

That is most likely just the include files, not the libraries

Francesco Cicconardi notifications@github.com writes:

I have them /home/tk19812/software/lzo-2.10/include

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594069343 I have them /home/tk19812/software/lzo-2.10/include

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francicco commented 4 years ago 
----------------------------------------------------------------------
Libraries have been installed in:
   /home/tk19812/software/lzo-2.10/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/home/tk19812/software/lzo-2.10/share/doc/lzo'
 /usr/bin/install -c -m 644 AUTHORS COPYING NEWS THANKS doc/LZO.FAQ doc/LZO.TXT doc/LZOAPI.TXT '/home/tk19812/software/lzo-2.10/share/doc/lzo'
 /usr/bin/mkdir -p '/home/tk19812/software/lzo-2.10/lib/pkgconfig'
 /usr/bin/install -c -m 644 lzo2.pc '/home/tk19812/software/lzo-2.10/lib/pkgconfig'
 /usr/bin/mkdir -p '/home/tk19812/software/lzo-2.10/include/lzo'
 /usr/bin/install -c -m 644 include/lzo/lzo1.h include/lzo/lzo1a.h include/lzo/lzo1b.h include/lzo/lzo1c.h include/lzo/lzo1f.h include/lzo/lzo1x.h include/lzo/lzo1y.h include/lzo/lzo1z.h include/lzo/lzo2a.h include/lzo/lzo_asm.h include/lzo/lzoconf.h include/lzo/lzodefs.h include/lzo/lzoutil.h '/home/tk19812/software/lzo-2.10/include/lzo'
/usr/bin/install: ‘include/lzo/lzo1.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1a.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1a.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1b.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1b.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1c.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1c.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1f.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1f.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1x.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1x.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1y.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1y.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1z.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1z.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo2a.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo2a.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo_asm.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo_asm.h’ are the same file
/usr/bin/install: ‘include/lzo/lzoconf.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzoconf.h’ are the same file
/usr/bin/install: ‘include/lzo/lzodefs.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzodefs.h’ are the same file
/usr/bin/install: ‘include/lzo/lzoutil.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzoutil.h’ are the same file
make[1]: *** [install-pkgincludeHEADERS] Error 1
make[1]: Leaving directory `/home/tk19812/software/lzo-2.10'
make: *** [install-am] Error 2
diekhans commented 4 years ago

The command output has -Wl,-rpath-link, having the include directory, not the lib directory.

Francesco Cicconardi notifications@github.com writes:

----------------------------------------------------------------------
Libraries have been installed in:
   /home/tk19812/software/lzo-2.10/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /usr/bin/mkdir -p '/home/tk19812/software/lzo-2.10/share/doc/lzo'
 /usr/bin/install -c -m 644 AUTHORS COPYING NEWS THANKS doc/LZO.FAQ doc/LZO.TXT doc/LZOAPI.TXT '/home/tk19812/software/lzo-2.10/share/doc/lzo'
 /usr/bin/mkdir -p '/home/tk19812/software/lzo-2.10/lib/pkgconfig'
 /usr/bin/install -c -m 644 lzo2.pc '/home/tk19812/software/lzo-2.10/lib/pkgconfig'
 /usr/bin/mkdir -p '/home/tk19812/software/lzo-2.10/include/lzo'
 /usr/bin/install -c -m 644 include/lzo/lzo1.h include/lzo/lzo1a.h include/lzo/lzo1b.h include/lzo/lzo1c.h include/lzo/lzo1f.h include/lzo/lzo1x.h include/lzo/lzo1y.h include/lzo/lzo1z.h include/lzo/lzo2a.h include/lzo/lzo_asm.h include/lzo/lzoconf.h include/lzo/lzodefs.h include/lzo/lzoutil.h '/home/tk19812/software/lzo-2.10/include/lzo'
/usr/bin/install: ‘include/lzo/lzo1.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1a.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1a.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1b.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1b.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1c.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1c.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1f.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1f.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1x.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1x.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1y.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1y.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo1z.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1z.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo2a.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo2a.h’ are the same file
/usr/bin/install: ‘include/lzo/lzo_asm.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo_asm.h’ are the same file
/usr/bin/install: ‘include/lzo/lzoconf.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzoconf.h’ are the same file
/usr/bin/install: ‘include/lzo/lzodefs.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzodefs.h’ are the same file
/usr/bin/install: ‘include/lzo/lzoutil.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzoutil.h’ are the same file
make[1]: *** [install-pkgincludeHEADERS] Error 1
make[1]: Leaving directory `/home/tk19812/software/lzo-2.10'
make: *** [install-am] Error 2

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/103#issuecomment-594070472---------------------------------------------------------------------- Libraries have been installed in: /home/tk19812/software/lzo-2.10/lib

If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following:

  • add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution
  • add LIBDIR to the 'LD_RUN_PATH' environment variable during linking
  • use the '-Wl,-rpath -Wl,LIBDIR' linker flag
  • have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages.

/usr/bin/mkdir -p '/home/tk19812/software/lzo-2.10/share/doc/lzo' /usr/bin/install -c -m 644 AUTHORS COPYING NEWS THANKS doc/LZO.FAQ doc/LZO.TXT doc/LZOAPI.TXT '/home/tk19812/software/lzo-2.10/share/doc/lzo' /usr/bin/mkdir -p '/home/tk19812/software/lzo-2.10/lib/pkgconfig' /usr/bin/install -c -m 644 lzo2.pc '/home/tk19812/software/lzo-2.10/lib/pkgconfig' /usr/bin/mkdir -p '/home/tk19812/software/lzo-2.10/include/lzo' /usr/bin/install -c -m 644 include/lzo/lzo1.h include/lzo/lzo1a.h include/lzo/lzo1b.h include/lzo/lzo1c.h include/lzo/lzo1f.h include/lzo/lzo1x.h include/lzo/lzo1y.h include/lzo/lzo1z.h include/lzo/lzo2a.h include/lzo/lzo_asm.h include/lzo/lzoconf.h include/lzo/lzodefs.h include/lzo/lzoutil.h '/home/tk19812/software/lzo-2.10/include/lzo' /usr/bin/install: ‘include/lzo/lzo1.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1.h’ are the same file /usr/bin/install: ‘include/lzo/lzo1a.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1a.h’ are the same file /usr/bin/install: ‘include/lzo/lzo1b.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1b.h’ are the same file /usr/bin/install: ‘include/lzo/lzo1c.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1c.h’ are the same file /usr/bin/install: ‘include/lzo/lzo1f.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1f.h’ are the same file /usr/bin/install: ‘include/lzo/lzo1x.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1x.h’ are the same file /usr/bin/install: ‘include/lzo/lzo1y.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1y.h’ are the same file /usr/bin/install: ‘include/lzo/lzo1z.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo1z.h’ are the same file /usr/bin/install: ‘include/lzo/lzo2a.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo2a.h’ are the same file /usr/bin/install: ‘include/lzo/lzo_asm.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzo_asm.h’ are the same file /usr/bin/install: ‘include/lzo/lzoconf.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzoconf.h’ are the same file /usr/bin/install: ‘include/lzo/lzodefs.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzodefs.h’ are the same file /usr/bin/install: ‘include/lzo/lzoutil.h’ and ‘/home/tk19812/software/lzo-2.10/include/lzo/lzoutil.h’ are the same file make[1]: [install-pkgincludeHEADERS] Error 1 make[1]: Leaving directory `/home/tk19812/software/lzo-2.10' make: [install-am] Error 2

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francicco commented 4 years ago

I don't understand