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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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install problem on Fedora 25 #21

Closed jblamyatifremer closed 7 years ago

jblamyatifremer commented 7 years ago

Dear ngmlr creator,

I am on fedora 25, 8 cores, 32 Gb of Ram. I also checked that all needed libraries have been installed namely (git wget gcc g++ libc6-dev make cmake zlib1g-dev) and checked in gcc > 4.9... But i failed to compile the ngmlr. I am sure that i have some dependency problems, but i can not found which library is missing.

During the install process : /usr/bin/ld : ne peut trouver [ENGLISH TRADUCTION : can't found] -lz /usr/bin/ld : ne peut trouver [ENGLISH TRADUCTION : can't found] -lpthread /usr/bin/ld : ne peut trouver [ENGLISH TRADUCTION : can't found] -lstdc++ /usr/bin/ld : ne peut trouver [ENGLISH TRADUCTION : can't found] -lm /usr/bin/ld : ne peut trouver [ENGLISH TRADUCTION : can't found] -lc collect2: erreur : ld a retourné 1 code d'état d'exécution [ENGLISH TRADUCTION :collect2: error: ld exit with error code : 1 ]

Below, I copy/paste the whole output :

[userlocal@lt-231 build]$ make [ 0%] Built target recompile_always Scanning dependencies of target ngmlr [ 3%] Building CXX object src/CMakeFiles/ngmlr.dir/AlignmentMatrix.cpp.o [ 7%] Building CXX object src/CMakeFiles/ngmlr.dir/AlignmentMatrixFast.cpp.o [ 11%] Building CXX object src/CMakeFiles/ngmlr.dir/ArgParser.cpp.o [ 15%] Building CXX object src/CMakeFiles/ngmlr.dir/CS.cpp.o [ 19%] Building CXX object src/CMakeFiles/ngmlr.dir/CSstatic.cpp.o [ 23%] Building CXX object src/CMakeFiles/ngmlr.dir/ConvexAlign.cpp.o [ 26%] Building CXX object src/CMakeFiles/ngmlr.dir/ConvexAlignFast.cpp.o [ 30%] Building CXX object src/CMakeFiles/ngmlr.dir/LinearRegression.cpp.o [ 34%] Building CXX object src/CMakeFiles/ngmlr.dir/Logging.cpp.o [ 38%] Building CXX object src/CMakeFiles/ngmlr.dir/MappedRead.cpp.o [ 42%] Building CXX object src/CMakeFiles/ngmlr.dir/main.cpp.o [ 46%] Building CXX object src/CMakeFiles/ngmlr.dir/NGM.cpp.o [ 50%] Building CXX object src/CMakeFiles/ngmlr.dir/NGMTask.cpp.o [ 53%] Building CXX object src/CMakeFiles/ngmlr.dir/AlignmentBuffer.cpp.o [ 57%] Building CXX object src/CMakeFiles/ngmlr.dir/PrefixTable.cpp.o [ 61%] Building CXX object src/CMakeFiles/ngmlr.dir/ReadProvider.cpp.o [ 65%] Building CXX object src/CMakeFiles/ngmlr.dir/SamParser.cpp.o [ 69%] Building CXX object src/CMakeFiles/ngmlr.dir/SAMWriter.cpp.o [ 73%] Building CXX object src/CMakeFiles/ngmlr.dir/SequenceProvider.cpp.o [ 76%] Building CXX object src/CMakeFiles/ngmlr.dir/OutputReadBuffer.cpp.o /home/userlocal/ngmlr/src/OutputReadBuffer.cpp: Dans le destructeur « OutputReadBuffer::~OutputReadBuffer() »: /home/userlocal/ngmlr/src/OutputReadBuffer.cpp:17:9: attention : throw will always call terminate() [-Wterminate] throw "Elements left in buffer!"; ^~~~~~ /home/userlocal/ngmlr/src/OutputReadBuffer.cpp:17:9: note : in C++11 destructors default to noexcept [ 80%] Building CXX object src/CMakeFiles/ngmlr.dir/ScoreBuffer.cpp.o [ 84%] Building CXX object src/CMakeFiles/ngmlr.dir/StrippedSW.cpp.o [ 88%] Building C object src/CMakeFiles/ngmlr.dir/__/lib/Complete-Striped-Smith-Waterman-Library/src/ssw.c.o [ 92%] Building CXX object src/CMakeFiles/ngmlr.dir/unix.cpp.o [ 96%] Building CXX object src/CMakeFiles/ngmlr.dir/unix_threads.cpp.o [100%] Linking CXX executable ../../bin/ngmlr-0.2.5-dev/ngmlr /usr/bin/ld : ne peut trouver -lz /usr/bin/ld : ne peut trouver -lpthread /usr/bin/ld : ne peut trouver -lstdc++ /usr/bin/ld : ne peut trouver -lm /usr/bin/ld : ne peut trouver -lc collect2: erreur : ld a retourné 1 code d'état d'exécution src/CMakeFiles/ngmlr.dir/build.make:719 : la recette pour la cible « ../bin/ngmlr-0.2.5-dev/ngmlr » a échouée make[2]: [../bin/ngmlr-0.2.5-dev/ngmlr] Erreur 1 CMakeFiles/Makefile2:124 : la recette pour la cible « src/CMakeFiles/ngmlr.dir/all » a échouée make[1]: [src/CMakeFiles/ngmlr.dir/all] Erreur 2 Makefile:129 : la recette pour la cible « all » a échouée make: *** [all] Erreur 2

JB

philres commented 7 years ago

Hi JB,

could you please download this already compiled binary and check whether it works for you?

https://github.com/philres/ngmlr/files/1084791/ngmlr-0.2.5-dev-beta-linux-x86_64.tar.gz

Thanks, Philipp

jblamyatifremer commented 7 years ago

It works perfectly...

I feel a bit idiot, since your README starts with "Download binary from github and unzip" I make my apologies.

A last question : It seems that ngmlr create a reference index on the fly (i do not find an equivalent of bwa index) ?

I close this thread. Thanks JB

fritzsedlazeck commented 7 years ago

Yes if there is no index already NGMLR will create one on the fly. Cheers Fritz

philres commented 7 years ago

Great happy to hear that!

Yes NGMLR creates an index consisting of the two following files:

-ht-13-2.2.ngm -enc.2.ngm Everything is done automatically, if the index does not exists NGMLR creates it. No need to build it manually. 2017-06-20 17:55 GMT+02:00 jblamyatifremer : > Closed #21 . > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > , or mute > the thread > > . >