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shendurelab / LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
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Issue with boost library during compiling LACHESIS #10

Closed kainblue closed 9 years ago

kainblue commented 9 years ago

I get another one with boost, I am using the latest one boost_1_59_0, do I need to switch to an older one too? Which version specifically?

g++ -Wall -ansi -pedantic -g -O3 TestMarkovModel.o SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o -o TestMarkovModel -lz -L/path/to/boost/boost_1_59_0/stage/lib -lboost_system -lboost_filesystem -lboost_regex

/usr/bin/ld: cannot find -lboost_system

/usr/bin/ld: cannot find -lboost_filesystem

/usr/bin/ld: cannot find -lboost_regex

collect2: error: ld returned 1 exit status

Makefile:40: recipe for target 'TestMarkovModel' failed

make[2]: *\ [TestMarkovModel] Error 1

make[2]: Leaving directory 'path/to/LACHESIS/include/markov'

Makefile:47: recipe for target 'libJmarkov.a' failed

make[1]: *\ [libJmarkov.a] Error 2

make[1]: Leaving directory '/path/to/LACHESIS/include'

Makefile:41: recipe for target 'libs' failed

make: *\ [libs] Error 2

makirc commented 9 years ago

It looks like your boost library might not be correctly installed, i.e. its path is probably not listed in LD_LIBRARY_PATH. Make sure that the boost lib sub folder is appended to LD_LIBRARY_PATH.

kainblue commented 9 years ago

So it does not related to the version? what is the LD_LIBRARY_PATH, do you mind showing me how do you set up the boost library?

Thanks a lot

makirc commented 9 years ago

No it should not depend on the version. You get a linker error and that just means that it does not find the pre-compiled libraries. Version problems usually come up during compilation, i.e. the step before linking.

So find out where your BOOST lib directly is. It is a sub directory of your boost installation. Mine is in a weird location, but let's assume it is in /home/user/bin/boost/1.52.0/lib/. LD_LIBRARY_PATH is a system variable, telling programs where to look for compiled libraries. You can check its current value with:

echo $LD_LIBRARY_PATH

Appending in bash works as follows:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: /home/user/bin/boost/1.52.0/lib/

Hope this helps.

kainblue commented 9 years ago

I just tried that but does not seems work. I will re-install the boost library and try it again. Another hypothesis is in the LACHESIS Makefile document, there are following several lines:

Includes

INCLUDE_DIR=include INCLUDES=-I$(INCLUDE_DIR) -I$(LACHESIS_SAMTOOLS_DIR)

Linking flags. The environment variables BOOST_LIBS and SAMTOOLS_LIBS must be set or this won't work.

INC_LIBS=-L$(INCLUDE_DIR) -lJtime -lJgtools -lJmarkov BOOST_LIBS=-L$(LACHESIS_BOOST_DIR)/stage/lib -lboost_system -lboost_filesystem -lboost_regex SAMTOOLS_LIBS=-L$(LACHESIS_SAMTOOLS_DIR) -lbam LFLAGS = $(INC_LIBS) $(BOOST_LIBS) $(SAMTOOLS_LIBS) -lz -lpthread

How many environment variables I need to set up? Can you show me how do you set up all the environment variables for LACHESIS?

Thanks

Bo

makirc commented 9 years ago

Good catch. I had assumed you had checked these things. I am also not familiar with the specifics of Lachesis, I am just providing general support here as Josh is not available right now. If boost was not in LD_LIBRARY_PATH, there is a good chance that you will still need it later on when executing Lachesis. So adding it was a good exercise.

You do not need to edit the Makefile, just use export for two other variables, like that:

export LACHESIS_SAMTOOLS_DIR=/path/to/compiled/samtools-0.1.19/ export LACHESIS_BOOST_DIR=/path/to/boost/

The boost path that you set should have stage/lib/ as a subfolder (containing the actual libraries), otherwise it will not work. The samtools folder is just the top level folder where you extracted samtools and ran make. It has for example the bam.h and bam.o files in it.

run make clean, before you run make again.

kainblue commented 9 years ago

Thank you so much for the help, actually I indeed realize that I need to manually create /stage/lib under boost to let the Lachesis make to happen. But later on I found out the rest of compiling will do the same thing for each .c file: g++ -c Lachesis.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0

I manually add the boost part as input directory for each of the .c file to be compiled otherwise it will complain that include <boost/xxx.hpp> not find.

After done that, I was exacted to run the testing LACHESIS on a sample dataset part, but the reality throw me down to the ground:

Lachesis: command not found

Here are the current files under my LACHESIS directory:

blast.qsub.sh ClusterVec.h CountMappables.pl GenomeLinkMatrix.o LinkSizeDistribution.cc QuickDotplot RunParams.cc TextFileParsers.o blast.sh ClusterVec.o CountMotifsInFasta.pl heatmap.MWAH.R LinkSizeDistribution.h QuickDotplot.POA.R RunParams.h TrueMapping.cc boost commentify_INIs.pl CreateScaffoldedFasta.pl heatmap.R LinkSizeDistribution.o QuickDotplot.SKY.R RunParams.o TrueMapping.h ChromLinkMatrix.cc contig Data Prep Flowchart.png include make_bed_around_RE_site.pl README.md splash_screen.txt TrueMapping.o ChromLinkMatrix.h ContigOrdering.cc decommentify_INIs.pl INIs Makefile Reporter.cc test_case ChromLinkMatrix.o ContigOrdering.h GenomeLinkMatrix.cc Lachesis.cc PreprocessSAMs.pl Reporter.h TextFileParsers.cc ClusterVec.cc ContigOrdering.o GenomeLinkMatrix.h Lachesis.o PreprocessSAMs.sh Reporter.o TextFileParsers.h

What else I need to do to make it run?

Thanks

makirc commented 9 years ago

The final linking step never happened. But let's step back a bit. Just generating an empty directory is not the solution nor is compiling the scripts separately. Do I understand correctly that

/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0

does contain a lib subfolder but not a stage/lib/ subfolder? Rather than generating empty ones, generate a symbolic link:

Remove the empty folder structure that you created

rm -R /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/stage/

Generate the stage folder that Lachesis expects

mkdir /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/stage/

Link the lib with the libraries to the stage folder

ln -s /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/lib /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/stage/lib

Do the exports:

export LACHESIS_SAMTOOLS_DIR=/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19/

export LACHESIS_BOOST_DIR=/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/

Retry make

make clean make all

kainblue commented 9 years ago

Sorry, I did not explain to you my current problem correctly. Actually here is what I did: For boost: After download from official website and unzip it, I find there is a "libs" folder under the main structure, but the contents are not the library files like this "libboost_atomic.so", so I build them by following their website instruction: http://www.boost.org/doc/libs/1_59_0/more/getting_started/unix-variants.html then I get a folder "lib" including all the ".so" or ".a" files. For LACHESIS: Since we find out that the error during the make is complaining about not finding the libraries in the /stage/lib path, so instead of making a soft link I actually make a subfolder "stage" and then copy all the files from the boost "lib" folder to stage, I did not just making a empty folder.

Now, when I run make, I can get almost all the way through, but just one remaining error:

make -C include make[1]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include' g++ -c TimeMem.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 ar crv libJtime.a TimeMem.o a - TimeMem.o make -C gtools make[2]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/gtools' g++ -c N50.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c ChromInterval.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c HumanGenome.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c CopyNumberProfile.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c FileParsers.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c SAMStepper.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 ar crv libJgtools.a N50.o ChromInterval.o HumanGenome.o CopyNumberProfile.o FileParsers.o SAMStepper.o; mv libJgtools.a .. a - N50.o a - ChromInterval.o a - HumanGenome.o a - CopyNumberProfile.o a - FileParsers.o a - SAMStepper.o make[2]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/gtools' make -C markov make[2]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/markov' g++ -c TestMarkovModel.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c SymbolSet.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c WDAG.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c MarkovModel.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c MarkovChain.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c HMM.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -Wall -ansi -pedantic -g -O3 TestMarkovModel.o SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o -o TestMarkovModel -lz -L/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/stage/lib -lboost_system -lboost_filesystem -lboost_regex ar crv libJmarkov.a SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o; mv libJmarkov.a .. a - SymbolSet.o a - WDAG.o a - MarkovModel.o a - MarkovChain.o a - HMM.o make[2]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/markov' make -C gtools make[2]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/gtools' ar crv libJgtools.a N50.o ChromInterval.o HumanGenome.o CopyNumberProfile.o FileParsers.o SAMStepper.o; mv libJgtools.a .. a - N50.o a - ChromInterval.o a - HumanGenome.o a - CopyNumberProfile.o a - FileParsers.o a - SAMStepper.o make[2]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/gtools' make -C markov make[2]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/markov' ar crv libJmarkov.a SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o; mv libJmarkov.a .. a - SymbolSet.o a - WDAG.o a - MarkovModel.o a - MarkovChain.o a - HMM.o make[2]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/markov' make[1]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include' g++ -c Lachesis.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 Lachesis.cc:46:32: fatal error: boost/filesystem.hpp: No such file or directory

include <boost/filesystem.hpp>

                            ^

compilation terminated. Makefile:36: recipe for target 'Lachesis.o' failed make: *\ [Lachesis.o] Error 1

I check the Lachesis.cc file, at the beginning it includes a bunch of library:

include

include

include

// STL declarations

include

include

include

include

include

include

using namespace std;

// Modules in ~/include (must add -L~/include and -lJ to link)

include "TimeMem.h"

// Boost includes

include <boost/filesystem.hpp>

include <boost/lexical_cast.hpp>

// Local includes

include "RunParams.h"

include "GenomeLinkMatrix.h"

include "ChromLinkMatrix.h"

include "LinkSizeDistribution.h"

include "ClusterVec.h"

include "ContigOrdering.h"

include "TrueMapping.h"

include "Reporter.h"

But I do not understand why it does not recognize <boost/XXXXX> If you notice the last compiling command in the make: g++ -c Lachesis.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 Lachesis.cc:46:32: fatal error: boost/filesystem.hpp: No such file or directory

My hypothesis is the make script did not including the boost path, so it can not recognize <boost/XXXX> in the include

How do I solve this? Do I need to modify the Makefile script? I never program in c++ before, can you help me with that?

Thanks a lot

makirc commented 9 years ago

Sorry for the trouble that you are having. Yes, try editing the Makefile and change:

INCLUDES=-I$(INCLUDE_DIR) -I$(LACHESIS_SAMTOOLS_DIR)

to

INCLUDES=-I$(INCLUDE_DIR) -I$(LACHESIS_SAMTOOLS_DIR) -I$(LACHESIS_BOOST_DIR)/include

Make sure that the path that you are defining as LACHESIS_BOOST_DIR actually has an include sub folder and that it contains the *.hpp files. Otherwise modify appropriately.

kainblue commented 9 years ago

Thanks a lot. This time seems compiling successfully except one warning about the data type "long"

make -C include make[1]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include' g++ -c TimeMem.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 ar crv libJtime.a TimeMem.o a - TimeMem.o make -C gtools make[2]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/gtools' g++ -c N50.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c ChromInterval.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c HumanGenome.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c CopyNumberProfile.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c FileParsers.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 g++ -c SAMStepper.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 ar crv libJgtools.a N50.o ChromInterval.o HumanGenome.o CopyNumberProfile.o FileParsers.o SAMStepper.o; mv libJgtools.a .. a - N50.o a - ChromInterval.o a - HumanGenome.o a - CopyNumberProfile.o a - FileParsers.o a - SAMStepper.o make[2]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/gtools' make -C markov make[2]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/markov' g++ -c TestMarkovModel.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c SymbolSet.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c WDAG.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c MarkovModel.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c MarkovChain.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c HMM.cc -Wall -ansi -pedantic -g -O3 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -Wall -ansi -pedantic -g -O3 TestMarkovModel.o SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o -o TestMarkovModel -lz -L/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/stage/lib -lboost_system -lboost_filesystem -lboost_regex ar crv libJmarkov.a SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o; mv libJmarkov.a .. a - SymbolSet.o a - WDAG.o a - MarkovModel.o a - MarkovChain.o a - HMM.o make[2]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/markov' make -C gtools make[2]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/gtools' ar crv libJgtools.a N50.o ChromInterval.o HumanGenome.o CopyNumberProfile.o FileParsers.o SAMStepper.o; mv libJgtools.a .. a - N50.o a - ChromInterval.o a - HumanGenome.o a - CopyNumberProfile.o a - FileParsers.o a - SAMStepper.o make[2]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/gtools' make -C markov make[2]: Entering directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/markov' ar crv libJmarkov.a SymbolSet.o WDAG.o MarkovModel.o MarkovChain.o HMM.o; mv libJmarkov.a .. a - SymbolSet.o a - WDAG.o a - MarkovModel.o a - MarkovChain.o a - HMM.o make[2]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include/markov' make[1]: Leaving directory '/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/shendurelab-LACHESIS-2151de9/include' g++ -c Lachesis.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c Reporter.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c ChromLinkMatrix.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 In file included from /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/boost/unordered/detail/table.hpp:15:0, from /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/boost/unordered/detail/equivalent.hpp:15, from /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/boost/unordered/unordered_set.hpp:18, from /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/boost/unordered_set.hpp:17, from /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/boost/graph/adjacency_list.hpp:21, from ChromLinkMatrix.cc:24: /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/boost/unordered/detail/buckets.hpp:703:29: warning: ISO C++ 1998 does not support ‘long long’ [-Wlong-long] struct pick_policy { ^ /afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/boost/unordered/detail/buckets.hpp:708:38: warning: ISO C++ 1998 does not support ‘long long’ [-Wlong-long] struct pick_policy { ^ g++ -c GenomeLinkMatrix.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c TrueMapping.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c LinkSizeDistribution.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c ContigOrdering.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c ClusterVec.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c RunParams.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -c TextFileParsers.cc -Wall -g -O3 -ansi -pedantic -Iinclude -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -I/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0 g++ -Wall -g -O3 -ansi -pedantic Lachesis.o Reporter.o ChromLinkMatrix.o GenomeLinkMatrix.o TrueMapping.o LinkSizeDistribution.o ContigOrdering.o ClusterVec.o RunParams.o TextFileParsers.o -o Lachesis -Linclude -lJtime -lJgtools -lJmarkov -L/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/boost_1_58_0/stage/lib -lboost_system -lboost_filesystem -lboost_regex -L/afs/bx.psu.edu/user/b/bkz5032/LACHESIS/samtools-0.1.19 -lbam -lz -lpthread

But when I am trying to run the test on sample dataset, it still says command not find

[bkz5032@promoter shendurelab-LACHESIS-2151de9]$ Lachesis INIs/test_case.ini -bash: Lachesis: command not found

Am I missing anything important here?

kainblue commented 9 years ago

Finally,

|~~~~~~~~~~|

| |

| |

| LACHESIS |

| |

| A software tool to measure the thread of life. |

| |

| |

| Created by Josh Burton, in the University of |

| Washington's Department of Genome Sciences |

| |

| Paper: http://dx.doi.org/10.1038/nbt.2727 |

| |

|~~~~~~~~~~|

Sat Sep 5 13:45:05 2015

Syntax: Lachesis

For a sample ini_file, see Lachesis.ini.

2015-09-05 12:41 GMT-04:00 makirc notifications@github.com:

Sorry for the trouble that you are having. Yes, try editing the Makefile and change:

INCLUDES=-I$(INCLUDE_DIR) -I$(LACHESIS_SAMTOOLS_DIR)

to

INCLUDES=-I$(INCLUDE_DIR) -I$(LACHESIS_SAMTOOLS_DIR) -I$(LACHESIS_BOOST_DIR)/include

Make sure that the path that you are defining as LACHESIS_BOOST_DIR actually has an include sub folder and that it contains the *.hpp files. Otherwise modify appropriately.

— Reply to this email directly or view it on GitHub https://github.com/shendurelab/LACHESIS/issues/10#issuecomment-137973230 .

kainblue commented 9 years ago

But when I run the test sample, I get this fault and stop in the middle:

Among the 9558 contigs aligned to canonical chromosomes... Number of contigs mis-clustered = 4561 of 9558 (47.7192%) Length of contigs mis-clustered = 1017203773 of 2512681042 (40.4828%) Number of informative contigs (used in clustering) mis-clustered = 2622 of 6643 (39.4701%) Length of informative contigs (used in clustering) mis-clustered = 961554907 of 2404827914 (39.9844%)

|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
|                                 |
|        LACHESIS ORDERING        |
|                                 |
|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|

Sat Sep 5 13:51:13 2015: Need to read SAM files and create ChromLinkMatrix files at out/test_case/cached_data/group*.CLM. This will take a while. Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 829 contigs (matrix size = 1658x1658) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 722 contigs (matrix size = 1444x1444) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 697 contigs (matrix size = 1394x1394) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 731 contigs (matrix size = 1462x1462) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 636 contigs (matrix size = 1272x1272) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 561 contigs (matrix size = 1122x1122) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 549 contigs (matrix size = 1098x1098) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 494 contigs (matrix size = 988x988) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 382 contigs (matrix size = 764x764) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 391 contigs (matrix size = 782x782) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 358 contigs (matrix size = 716x716) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 347 contigs (matrix size = 694x694) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 318 contigs (matrix size = 636x636) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 359 contigs (matrix size = 718x718) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 334 contigs (matrix size = 668x668) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 271 contigs (matrix size = 542x542) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 279 contigs (matrix size = 558x558) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 291 contigs (matrix size = 582x582) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 218 contigs (matrix size = 436x436) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 249 contigs (matrix size = 498x498) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 208 contigs (matrix size = 416x416) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 251 contigs (matrix size = 502x502) Sat Sep 5 13:51:13 2015: Creating a new ChromLinkMatrix for a cluster with 238 contigs (matrix size = 476x476) Sat Sep 5 13:51:13 2015: Filling 23 clusters with Hi-C data from SAM file test_case/SAMs/SRR400260.sample.bam (dot = 1M alignments)

Sat Sep 5 13:51:14 2015: Filling 23 clusters with Hi-C data from SAM file test_case/SAMs/SRR400261.sample.bam (dot = 1M alignments)

Sat Sep 5 13:51:14 2015: Filling 23 clusters with Hi-C data from SAM file test_case/SAMs/SRR400262.sample.bam (dot = 1M alignments)

Sat Sep 5 13:51:14 2015: Filling 23 clusters with Hi-C data from SAM file test_case/SAMs/SRR400263.sample.bam (dot = 1M alignments)

Sat Sep 5 13:51:14 2015: Filling 23 clusters with Hi-C data from SAM file test_case/SAMs/SRR442155.sample.bam (dot = 1M alignments)

Sat Sep 5 13:51:14 2015: Filling 23 clusters with Hi-C data from SAM file test_case/SAMs/SRR442156.sample.bam (dot = 1M alignments)

Sat Sep 5 13:51:14 2015: Filling 23 clusters with Hi-C data from SAM file test_case/SAMs/SRR442157.sample.bam (dot = 1M alignments)

Sat Sep 5 13:51:14 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group0.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group1.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group2.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group3.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group4.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group5.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group6.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group7.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group8.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group9.CLM Sat Sep 5 13:51:15 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group10.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group11.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group12.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group13.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group14.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group15.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group16.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group17.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group18.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group19.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group20.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group21.CLM Sat Sep 5 13:51:16 2015: ChromLinkMatrix::WriteFile(CLM) -> out/test_case/cached_data/group22.CLM Sat Sep 5 13:51:16 2015: Ordering on cluster #0 Segmentation fault

makirc commented 9 years ago

Sounds like you ran into an previously reported issue: https://github.com/shendurelab/LACHESIS/issues/1

I am closing out this one. I hope that Josh will look into that once he returns from vacation. I will also check with another lab member who has actually used Lachesis.

kainblue commented 9 years ago

Ok, thanks a lot.

2015年9月5日星期六，makirc notifications@github.com 写道：

Sounds like you ran into an previously reported issue: #1 https://github.com/shendurelab/LACHESIS/issues/1

I am closing out this one. I hope that Josh will look into that once he returns from vacation. I will also check with another lab member who has actually used Lachesis.

— Reply to this email directly or view it on GitHub https://github.com/shendurelab/LACHESIS/issues/10#issuecomment-138039066 .