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lbcb-sci / graphmap2

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1
MIT License
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fail to install the graphmap2 v0.6.4 #16

Open sen1019san opened 3 years ago

sen1019san commented 3 years ago

Hi, I am trying to install graphmap2 in linux server (ubuntu16.04.12). After successfully executing the "make modual" step, I failed in the "make" step. Here shows the error information:

Makefile:100: " WARNING /home/lhs/miniconda3/bin/x86_64-conda-linux-gnu-gcc minor version <7 " mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/ /home/lhs/miniconda3/bin/x86_64-conda-linux-gnu-gcc -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/gindex/src -Icodebase/seqlib/src -Icodebase/argumentparser/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp In file included from codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort_private.h:33:0, from codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp:29: /usr/include/stdlib.h:759:11: fatal error: bits/stdlib-bsearch.h: No such file or directory include <bits/stdlib-bsearch.h> ^~~~~~~ compilation terminated. **make: * [Makefile:128: obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o] Error 1

Thanks a lot for any help.

jmaricb commented 3 years ago

Hi,

What are the steps you used to build the program? Let me know so I can see what the error could be.

Also what is the command you use to map reads to the reference? If you are trying to map RNA reads you have to use -x rnaseq option. If you are mapping DNA reads, you can try old Graphmap since it is the same for DNA reads as this one.

sen1019san commented 3 years ago

Thanks, @jmaricb. I failed in the "make" step in installing graphmap2 (v0.6.4). The error information is shown above. Then I installed the v0.6.3 version by bioconda and it worked.

jmaricb commented 3 years ago

I am not sure why the make command fails, maybe something with the compiler version on your machine.

Tell me, are you running the command with '-x rnaseq' parameter?

sen1019san commented 3 years ago

Thanks, @jmaricb. I am trying to map the DNA read. But no reads are aligned against the reference genome. Similar problem is described by issue #10 .

jmaricb commented 3 years ago

Hi,

use the previous version of Graphmap: https://github.com/isovic/graphmap

There is no difference for the DNA reads in Graphmap2, and the previous version will work.

sen1019san commented 3 years ago

Thanks, @jmaricb. I will try to use the previous version.