Hello
I have installed from bioconda and everything seems to be going well until I get to the FastTreeMP step:, where I get
“phylophlan_output/tmp/sub/p0011.aln” generated in 0s
“phylophlan_output/tmp/sub/p0303.aln” generated in 0s
Concatenating alignments
Alignments concatenated “phylophlan_output/pi_concatenated.aln” in 0s
Building phylogeny “phylophlan_output/pi_concatenated.aln”
[e] Command ‘[’/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/phylophlan/bin/FastTreeMP’, ‘-quiet’, ‘-pseudo’, ‘-spr’, ‘4’, ‘-mlacc’, ‘2’, ‘-slownni’, ‘-fastest’, ‘-no2nd’, ‘-mlnni’, ‘4’, ‘-lg’, ‘-out’, ‘/exports/cmvm/eddie/eb/groups/watson_grp/11690_Watson_Mick/MAGS/phylophlan_output/pi.tre’, ‘phylophlan_output/pi_concatenated.aln’]’ returned non-zero exit status 1.
[e] error while executing
command_line: /exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/phylophlan/bin/FastTreeMP -quiet -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /exports/cmvm/eddie/eb/groups/watson_grp/11690_Watson_Mick/MAGS/phylophlan_output/pi.tre phylophlan_output/pi_concatenated.aln
stdin: None
stdout: None
env: {‘MODULE_VERSION_STACK’: ‘3.2.10’, ‘MANPATH’: ‘/exports/applications/apps/SL7/anaconda/5.0.1/share/man:/exports/applications/gridengine/ge-8.6.5/man:/usr/share/man/overrides:/usr/share/man:/usr/local/share/man’, ‘XDG_SESSION_ID’: ‘38947’, ‘HOSTNAME’: ‘node2i15.ecdf.ed.ac.uk’, ‘SHELL’: ‘/bin/bash’, ‘TERM’: ‘xterm’, ‘HISTSIZE’: ‘1000’, ‘SGE_JSV_TIMEOUT’: ‘30’, ‘SSH_CLIENT’: ‘192.41.104.221 55502 22’, ‘NCBI_BLASTBIN’: ‘/exports/igmm/software/pkg/el7/apps/ncbi_blast/2.4.0/bin’, ‘NCARG_FONTCAPS’: ‘/usr/lib64/ncarg/fontcaps’, ‘SGE_CELL’: ‘eddieUGE’, ‘PERL_MB_OPT’: ‘–install_base /home/mwatson9/perl5’, ‘SSH_TTY’: ‘/dev/pts/1’, ‘QT_GRAPHICSSYSTEM_CHECKED’: ‘1’, ‘USER’: ‘mwatson9’, ‘NVM_DIR’: ‘/home/mwatson9/.nvm’, ‘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=01;05;37;41: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:.Z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=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:.jpg=01;35:.jpeg=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:.axv=01;35:.anx=01;35:.ogv=01;35:.ogx=01;35:.aac=01;36:.au=01;36:.flac=01;36:.mid=01;36:.midi=01;36:.mka=01;36:.mp3=01;36:.mpc=01;36:.ogg=01;36:.ra=01;36:.wav=01;36:.axa=01;36:.oga=01;36:.spx=01;36:*.xspf=01;36::di=0;36:fi=0;32:ln=0;35;or=0;31’, ‘KEYNAME’: ‘id_alcescluster’, ‘NCARG_GRAPHCAPS’: ‘/usr/lib64/ncarg/graphcaps’, ‘ED’: ‘/exports/cmvm/eddie/eb/groups/watson_grp/’, ‘PATH’: ‘/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/phylophlan/bin:/exports/applications/apps/SL7/anaconda/5.0.1/bin:/exports/igmm/software/pkg/el7/apps/ncbi_blast/2.4.0/bin:/exports/cmvm/eddie/eb/groups/watson_grp/software/minimap2/:/exports/cmvm/eddie/eb/groups/watson_grp/software/miniasm/:/exports/cmvm/eddie/eb/groups/watson_grp/software/kallisto_linux-v0.43.0/:/exports/cmvm/eddie/eb/groups/watson_grp/software/snakemake_groupfolder/shells/:/exports/cmvm/eddie/eb/groups/watson_grp/software/canu_hacks/:/home/mwatson9/perl5/bin:/exports/applications/gridengine/ge-8.6.5/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/exports/cmvm/eddie/eb/groups/watson_grp/snakemake_assembly/shells:/exports/cmvm/eddie/eb/groups/watson_grp/snakemake_testing/shells:/exports/cmvm/eddie/eb/groups/watson_grp/software/prodigal/:/home/mwatson9/.local/bin:/home/mwatson9/bin’, ‘MAIL’: ‘/var/spool/mail/mwatson9’, ‘MODULE_VERSION’: ‘3.2.10’, ‘CONDA_PATH_BACKUP’: ‘/exports/applications/apps/SL7/anaconda/5.0.1/bin:/exports/igmm/software/pkg/el7/apps/ncbi_blast/2.4.0/bin:/exports/cmvm/eddie/eb/groups/watson_grp/software/minimap2/:/exports/cmvm/eddie/eb/groups/watson_grp/software/miniasm/:/exports/cmvm/eddie/eb/groups/watson_grp/software/kallisto_linux-v0.43.0/:/exports/cmvm/eddie/eb/groups/watson_grp/software/snakemake_groupfolder/shells/:/exports/cmvm/eddie/eb/groups/watson_grp/software/canu_hacks/:/home/mwatson9/perl5/bin:/exports/applications/gridengine/ge-8.6.5/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/exports/cmvm/eddie/eb/groups/watson_grp/snakemake_assembly/shells:/exports/cmvm/eddie/eb/groups/watson_grp/snakemake_testing/shells:/exports/cmvm/eddie/eb/groups/watson_grp/software/prodigal/:/home/mwatson9/.local/bin:/home/mwatson9/bin’, ‘_’: ‘/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/phylophlan/bin/phylophlan’, ‘DS’: ‘/exports/cmvm/datastore/eb/groups/watson_grp/’, ‘CONDA_PREFIX’: ‘/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/phylophlan’, ‘PWD’: ‘/exports/cmvm/eddie/eb/groups/watson_grp/11690_Watson_Mick/MAGS’, ‘NCARG_ROOT’: ‘/usr’, ‘LMFILES’: ‘/exports/applications/modulefiles/Community/igmm/apps/ncbi_blast/2.4.0:/exports/applications/modulefiles/SL7/Applications/anaconda/5.0.1’, ‘SGE_EXECD_PORT’: ‘6445’, ‘LANG’: ‘en_GB.UTF-8’, ‘MODULEPATH’: ‘/exports/applications/modulefiles/SL7/Tools:/exports/applications/modulefiles/SL7/Compilers:/exports/applications/modulefiles/SL7/Libraries:/exports/applications/modulefiles/SL7/Applications:/exports/applications/modulefiles/Community:/exports/igmm/software/etc/el7/modules’, ‘NCARG_DATABASE’: ‘/usr/lib64/ncarg/database’, ‘SGE_QMASTER_PORT’: ‘6444’, ‘KDEDIRS’: ‘/usr’, ‘LOADEDMODULES’: ‘igmm/apps/ncbi_blast/2.4.0:anaconda/5.0.1’, ‘SGE_ROOT’: ‘/exports/applications/gridengine/ge-8.6.5’, ‘SKIP_USERS’: ‘root alces’, ‘USE_SYSTEMD’: ‘false’, ‘HISTCONTROL’: ‘ignoredups’, ‘NCARG_LIB’: ‘/usr/lib64/ncarg’, ‘HOME’: ‘/home/mwatson9’, ‘SHLVL’: ‘1’, ‘NCARG_NCARG’: ‘/usr/share/ncarg’, ‘NCBI_BLASTDIR’: ‘/exports/igmm/software/pkg/el7/apps/ncbi_blast/2.4.0’, ‘DRMAA_LIBRARY_PATH’: ‘/opt/sge/lib/lx-amd64/libdrmaa.so’, ‘CONDA_PS1_BACKUP’: '[\u@\h\[\e1;34m\\[\e[0m\] \W]\$ ', ‘PERL_LOCAL_LIB_ROOT’: ‘:/home/mwatson9/perl5’, ‘LOGNAME’: ‘mwatson9’, ‘CVS_RSH’: ‘ssh’, ‘SSH_CONNECTION’: ‘192.41.104.221 55502 192.41.105.222 22’, ‘LOG’: ‘/home/mwatson9/eddie3-login.log’, ‘MODULESHOME’: ‘/exports/applications/apps/SL7/environment-modules-3.2.10/Modules/3.2.10’, ‘LESSOPEN’: ‘||/usr/bin/lesspipe.sh %s’, ‘CONDA_DEFAULT_ENV’: ‘phylophlan’, ‘LOWEST_UID’: ‘500’, ‘DISPLAY’: ‘localhost:10.0’, ‘XDG_RUNTIME_DIR’: ‘/run/user/600551’, ‘SGE_CLUSTER_NAME’: ‘eddie’, ‘QT_PLUGIN_PATH’: ‘/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins’, ‘SCRATCH’: ‘/exports/eddie/scratch/mwatson9/’, ‘PERL_MM_OPT’: ‘INSTALL_BASE=/home/mwatson9/perl5’, ‘SSHHOME’: ‘/home/mwatson9/.ssh/’, ‘BASH_FUNC_module()’: ‘() { eval /exports/applications/apps/SL7/environment-modules-3.2.10/Modules/$MODULE_VERSION/bin/modulecmd bash $*\n}’, ‘OMP_NUM_THREADS’: ‘3’}
The command line it claims to want to run is:
FastTreeMP -quiet -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /exports/cmvm/eddie/eb/groups/watson_grp/11690_Watson_Mick/MAGS/phylophlan_output/pi.tre phylophlan_output/pi_concatenated.aln
When I run this, I get:
Unknown or incorrect use of option -lg
FastTree protein_alignment > tree
FastTree < protein_alignment > tree
FastTree -out tree protein_alignment
FastTree -nt nucleotide_alignment > tree
FastTree -nt -gtr < nucleotide_alignment > tree
FastTree < nucleotide_alignment > tree
FastTree accepts alignments in fasta or phylip interleaved formats
Any ideas?
