Hello everyone,
I am currently using Phylophlan 3.0.67 using the data from S.aureus tutorial available.
I am experiencing an error just in the last part of the tutorial, when using raxml.
This is the error that I get:
"Setting RAxML threads to 2, cannot use 1 thread with RAxML parallel version
[e] Command ‘[’/usr/bin/raxmlHPC-PTHREADS-SSE3’, ‘-p’, ‘1989’, ‘-m’, ‘GTRCAT’, ‘-T’, ‘2’, ‘-t’, ‘output_references/input_references_resolved.tre’, ‘-w’, ‘/home/minluke/output_references’, ‘-s’, ‘output_references/input_references_concatenated.aln’, ‘-n’, ‘input_references_refined.tre’]’ returned non-zero exit status 255.
[e] error while executing
command_line: /usr/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m GTRCAT -T 2 -t output_references/input_references_resolved.tre -w /home/minluke/output_references -s output_references/input_references_concatenated.aln -n input_references_refined.tre
stdin: None
stdout: None
env: {‘SHELL’: ‘/bin/bash’, ‘DEBUG_FFLAGS’: ‘-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/minluke/miniconda/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe’, ‘GCC_RANLIB’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gcc-ranlib’, ‘CONDA_EXE’: ‘/home/minluke/miniconda/bin/conda’, ‘_CE_M’: ‘’, ‘WSL_DISTRO_NAME’: ‘Ubuntu-20.04’, ‘build_alias’: ‘x86_64-conda-linux-gnu’, ‘CMAKE_ARGS’: ‘-DCMAKE_AR=/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-strip’, ‘GPROF’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gprof’, ‘JAVA_HOME’: ‘/home/minluke/miniconda’, ‘CONDA_TOOLCHAIN_BUILD’: ‘x86_64-conda-linux-gnu’, ‘_CONDA_PYTHON_SYSCONFIGDATA_NAME’: ‘_sysconfigdata_x86_64_conda_cos6_linux_gnu’, ‘STRINGS’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-strings’, ‘CPP’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-cpp’, ‘JAVA_LD_LIBRARY_PATH’: ‘/home/minluke/miniconda/lib/server’, ‘FFLAGS’: ‘-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/minluke/miniconda/include’, ‘NAME’: ‘LAPTOP-HRKMQ4T6’, ‘PWD’: ‘/home/minluke’, ‘LOGNAME’: ‘minluke’, ‘CONDA_PREFIX’: ‘/home/minluke/miniconda’, ‘CXX’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-c++’, ‘CXXFLAGS’: ‘-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/minluke/miniconda/include’, ‘CONDA_TOOLCHAIN_HOST’: ‘x86_64-conda-linux-gnu’, ‘DEBUG_CXXFLAGS’: ‘-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/minluke/miniconda/include’, ‘MOTD_SHOWN’: ‘update-motd’, ‘LDFLAGS’: ‘-Wl,-O2 -Wl,–sort-common -Wl,–as-needed -Wl,-z,relro -Wl,-z,now -Wl,–disable-new-dtags -Wl,–gc-sections -Wl,–allow-shlib-undefined -Wl,-rpath,/home/minluke/miniconda/lib -Wl,-rpath-link,/home/minluke/miniconda/lib -L/home/minluke/miniconda/lib’, ‘CONDA_BACKUP_JAVA_HOME’: ‘:-’, ‘HOME’: ‘/home/minluke’, ‘LANG’: ‘C.UTF-8’, ‘WSL_INTEROP’: ‘/run/WSL/9_interop’, ‘DEBUG_CFLAGS’: ‘-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/minluke/miniconda/include’, ‘LS_COLORS’: ‘rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.zst=01;31:.tzst=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.wim=01;31:.swm=01;31:.dwm=01;31:.esd=01;31:.jpg=01;35:.jpeg=01;35:.mjpg=01;35:.mjpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:*.xspf=00;36:’, ‘CXX_FOR_BUILD’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-c++’, ‘ELFEDIT’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-elfedit’, ‘CONDA_PROMPT_MODIFIER’: '(base) ', ‘CMAKE_PREFIX_PATH’: ‘/home/minluke/miniconda:/home/minluke/miniconda/x86_64-conda-linux-gnu/sysroot/usr’, ‘CPPFLAGS’: ‘-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/minluke/miniconda/include’, ‘LD’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-ld’, ‘READELF’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-readelf’, ‘GXX’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-g++’, ‘FC_FOR_BUILD’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gfortran’, ‘GCC_AR’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gcc-ar’, ‘LESSCLOSE’: ‘/usr/bin/lesspipe %s %s’, ‘ADDR2LINE’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-addr2line’, ‘TERM’: ‘xterm-256color’, ‘CE_CONDA’: ‘’, ‘GCC_NM’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gcc-nm’, ‘SIZE’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-size’, ‘F77’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gfortran’, ‘HOST’: ‘x86_64-conda-linux-gnu’, ‘LESSOPEN’: ‘| /usr/bin/lesspipe %s’, ‘CC_FOR_BUILD’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-cc’, ‘USER’: ‘minluke’, ‘CONDA_SHLVL’: ‘1’, ‘AR’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-ar’, ‘AS’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-as’, ‘DEBUG_CPPFLAGS’: ‘-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/minluke/miniconda/include’, ‘F95’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-f95’, ‘F90’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gfortran’, ‘host_alias’: ‘x86_64-conda-linux-gnu’, ‘SHLVL’: ‘0’, ‘NM’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-nm’, ‘GCC’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gcc’, ‘DEBUG_FORTRANFLAGS’: ‘-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/minluke/miniconda/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe’, ‘FORTRANFLAGS’: ‘-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/minluke/miniconda/include’, ‘LD_GOLD’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-ld.gold’, ‘CONDA_PYTHON_EXE’: ‘/home/minluke/miniconda/bin/python’, ‘CONDA_BACKUP_JAVA_LD_LIBRARY_PATH’: ‘:-’, ‘GFORTRAN’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gfortran’, ‘CONDA_DEFAULT_ENV’: ‘base’, ‘OBJCOPY’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-objcopy’, ‘WSLENV’: ‘’, ‘FC’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-gfortran’, ‘STRIP’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-strip’, ‘XDG_DATA_DIRS’: ‘/usr/local/share:/usr/share:/var/lib/snapd/desktop’, ‘OBJDUMP’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-objdump’, ‘PATH’: ‘trimal:trimAl/source/:/home/minluke/.local/bin:/home/minluke/miniconda/bin:/home/minluke/miniconda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/TPP/cgi-bin:/mnt/c/TPP/perl/bin:/mnt/c/Perl64/bin:/mnt/c/Users/minluke/AppData/Roaming/ActiveState/bin:/mnt/c/Program Files/AdoptOpenJDK/jdk-11.0.9.101-hotspot/bin:/mnt/c/Program Files (x86)/Common Files/Oracle/Java/javapath:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Program Files/Intel/WiFi/bin:/mnt/c/Program Files/Common Files/Intel/WirelessCommon:/mnt/c/ProgramData/chocolatey/bin:/mnt/c/Program Files/Java/jdk1.8.0_211/bin:/mnt/c/Program Files/PuTTY:/mnt/c/Program Files/Git/cmd:/mnt/c/Go/bin:/mnt/c/Program Files/TortoiseHg:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program Files/dotnet:/mnt/c/Windows/System32:/mnt/c/TPP/bin:/mnt/c/TPP/perl/site/bin:/mnt/c/Program Files/010 Editor:/mnt/c/Program Files/Docker/Docker/resources/bin:/mnt/c/Program Files/NCBI/blast-2.12.0+/bin:/mnt/c/Users/minluke/AppData/Local/Programs/Microsoft VS Code/bin:/mnt/c/Users/minluke/go/bin:/mnt/c/Users/minluke/Desktop/jdk-11.0.9.1+1:/mnt/c/Users/minluke/AppData/Local/Microsoft/WindowsApps:/snap/bin’, ‘CC’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-cc’, ‘CFLAGS’: ‘-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/minluke/miniconda/include’, ‘CXXFILT’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-c++filt’, ‘BUILD’: ‘x86_64-conda-linux-gnu’, ‘HOSTTYPE’: ‘x86_64’, ‘RANLIB’: ‘/home/minluke/miniconda/bin/x86_64-conda-linux-gnu-ranlib’, ‘CONDA_BUILD_SYSROOT’: ‘/home/minluke/miniconda/x86_64-conda-linux-gnu/sysroot’, '’: ‘/home/minluke/miniconda/bin/phylophlan’}
"
I have also tried to run the command indicated alone, thus: “raxmlHPC-PTHREADS-SSE3 -p 1989 -m GTRCAT -T 2 -t output_references/input_references_resolved.tre -w output_references -s output_references/input_references_concatenated.aln -n input_references_refined.tre”
But I get the following error message : "Warning, you specified a working directory via “-w”
Keep in mind that RAxML only accepts absolute path names, not relative ones!
RAxML can’t, parse the alignment file as phylip file
it will now try to parse it as FASTA file
ERROR: Bad base (E) at site 1 of sequence 1"
How can I solve this issue? thank you a lot for your support in advance