fail to install the graphmap2 v0.6.4

[sen1019san]

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]

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]

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]

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]

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]

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]

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