I am assembling a plant genome using ABySS 2.0 short-read assembler. I am using the GitHub documentation to perform the installation of ABySS 2.0. I used Homebrew for installing ABySS, gcc, and all other dependencies, mentioned in the documentation.
Query After running the following script, I haven't been able to make progress.
./autogen.sh
mkdir build
cd build
../configure --prefix=/path/to/abyss
Here, --prefix= was set with path to a folder where I wanted to install ABySS. When I ran, It showed the following error.
checking for g++ -std=c++11 option to support OpenMP... -fopenmp
configure: error: ABySS requires the btllib C++ libraries, which may
be downloaded from here: https://github.com/bcgsc/btllib
It is necessary to compile btllib. The readme
in the GitHub repo contains instructs to compile btllib.
I installed btllib-1.7.0.tar.gz from this GitHub site, compiled then entered the following commands on the console.
export CPPFLAGS="-isystem home/palmyra/abyss/btllib-1.7.0/install/include $CPPFLAGS"
export LDFLAGS="-L/home/palmyra/abyss/btllib-1.7.0/install/lib -lbtllib $LDFLAGS"
After this, when I ran the ../configure --prefix=/path/to/abyss
it shows C++ compiler cannot create executables
the complete error:
checking for g++... g++
checking whether the C++ compiler works... no
configure: error: in '/home/palmyra/abyss/build':
configure: error: C++ compiler cannot create executables
The configure.log file can be accessed at here
Can someone help to troubleshoot it. I am very much confused.
====================================================================
EDIT: I removed the LDFLAGS and now C++ compiler creates executables. Currently, btllib-1.7 is not able to be compiled. I don't understand if it is because C++ compiler used for compiling Python matches the one used for compiling btllib.
Compiling btllib-1.7 shows the following error.
./../home/palmyra/abyss/btllib-1.7.0/include/btllib/hashing_internals.hpp:2896:11: error: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’ [-Werror=c++17-extensions]
2896 | constexpr inline const uint64_t*
| ^~~~~~
../../home/palmyra/abyss/btllib-1.7.0/include/btllib/hashing_internals.hpp:3156:11: error: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’ [-Werror=c++17-extensions]
3156 | constexpr inline const uint64_t* const LEVEL_X_AA_SEED_TABLE[4] = {
| ^~~~~~
../../home/palmyra/abyss/btllib-1.7.0/include/btllib/hashing_internals.hpp:3162:11: error: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’ [-Werror=c++17-extensions]
3162 | constexpr inline const uint64_t* const*
| ^~~~~~
../../home/palmyra/abyss/btllib-1.7.0/include/btllib/hashing_internals.hpp:3169:11: error: inline variables are only available with ‘-std=c++17’ or ‘-std=gnu++17’ [-Werror=c++17-extensions]
3169 | constexpr inline const uint64_t* const*
| ^~~~~~
In file included from ../../home/palmyra/abyss/btllib-1.7.0/include/btllib/nthash.hpp:13:
../../home/palmyra/abyss/btllib-1.7.0/include/btllib/nthash_kmer.hpp:14:11: error: nested namespace definitions only available with ‘-std=c++17’ or ‘-std=gnu++17’ [-Werror=c++17-extensions]
14 | namespace btllib::hashing_internals {
| ^~~~~~
In file included from ../../home/palmyra/abyss/btllib-1.7.0/include/btllib/nthash.hpp:14:
../../home/palmyra/abyss/btllib-1.7.0/include/btllib/nthash_seed.hpp:15:11: error: nested namespace definitions only available with ‘-std=c++17’ or ‘-std=gnu++17’ [-Werror=c++17-extensions]
15 | namespace btllib::hashing_internals {
| ^~~~~~
cc1plus: all warnings being treated as errors
ninja: build stopped: subcommand failed.
Traceback (most recent call last):
File "/home/palmyra/abyss/btllib-1.7.0/./compile", line 182, in <module>
sp.run(
File "/usr/lib/python3.11/subprocess.py", line 571, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['\n if [ -f /tmp/btllib-build-eLg_1lWEQkGwS9dB7HujlQ/venv/bin/activate ]; then\n . /tmp/btllib-build-eLg_1lWEQkGwS9dB7HujlQ/venv/bin/activate;\n fi &&\n export AR=gcc-ar &&\n meson setup --buildtype release -Db_lto=true -Db_ndebug=true -Db_coverage=false --prefix=/home/palmyra/abyss/btllib-1.7.0/install /tmp/btllib-build-eLg_1lWEQkGwS9dB7HujlQ &&\n cd /tmp/btllib-build-eLg_1lWEQkGwS9dB7HujlQ &&\n ninja install &&\n cd .. &&\n if [ -f /tmp/btllib-build-eLg_1lWEQkGwS9dB7HujlQ/venv/bin/activate ]; then\n deactivate;\n fi\n ']' returned non-zero exit status 1.
This is the compile Python file
you asked many questions but validated none (check on the left). For example: I have performed Trimmomatic run for adapter removal. QC report shows drop in the reads and presence of overrepresented sequences. Seeking help! . Please review or/and comment all your previous questions.