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Error running FastTreeMP step

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?

I can confirm that simply removing the “-lg” flag ensures that FastTreeMP runs and creates the desired .tre file

Hi, and thanks for reporting this.
The -lg parameter in FastTree is used for specifying the LG substitution model.

Can you please report the (1) the version of FastTreeMP, (2) the command you used for generating the configuration file and (3) the command you used for running PhyloPhlAn?

Many thanks,
Francesco

Hello!

The command was:

phylophlan -i pi -o phylophlan_output -d phylophlan --nproc 16 --diversity high --fast -f phylophlan_configs/supermatrix_aa.cfg --min_num_entries 2

The conda env was created using:

conda create -n phylophlan phylophlan

I am using supermatrix_aa.cfg which comes with PhyloPhlAn

Input dir “pi” is a directory containing two protein multi-fasta files of prodigal predicted amino acid sequences

Info on the conda env is:

packages in environment at /exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/phylophlan:

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
biopython 1.78 py39hbd71b63_1 conda-forge
blast 2.10.1 pl526he19e7b1_3 bioconda
boost-cpp 1.70.0 h7b93d67_3 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h36c2ea0_0 conda-forge
ca-certificates 2020.12.5 ha878542_0 conda-forge
certifi 2020.12.5 py39hf3d152e_0 conda-forge
curl 7.71.1 he644dc0_8 conda-forge
cycler 0.10.0 py_2 conda-forge
dendropy 4.5.1 pyh3252c3a_0 bioconda
diamond 2.0.5 h56fc30b_0 bioconda
entrez-direct 13.9 pl526h375a9b1_0 bioconda
expat 2.2.9 he1b5a44_2 conda-forge
fasttree 2.1.8 0 biocore
freetype 2.10.4 h7ca028e_0 conda-forge
icu 67.1 he1b5a44_0 conda-forge
iqtree 2.0.3 h176a8bc_0 bioconda
jpeg 9d h36c2ea0_0 conda-forge
kiwisolver 1.3.1 py39h081fc7a_0 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
lcms2 2.11 hcbb858e_1 conda-forge
ld_impl_linux-64 2.35.1 hed1e6ac_0 conda-forge
libblas 3.9.0 3_openblas conda-forge
libcblas 3.9.0 3_openblas conda-forge
libcurl 7.71.1 hcdd3856_8 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 9.3.0 h5dbcf3e_17 conda-forge
libgfortran-ng 9.3.0 he4bcb1c_17 conda-forge
libgfortran5 9.3.0 he4bcb1c_17 conda-forge
libgomp 9.3.0 h5dbcf3e_17 conda-forge
liblapack 3.9.0 3_openblas conda-forge
libnghttp2 1.41.0 h8cfc5f6_2 conda-forge
libopenblas 0.3.12 pthreads_h4812303_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libssh2 1.9.0 hab1572f_5 conda-forge
libstdcxx-ng 9.3.0 h2ae2ef3_17 conda-forge
libtiff 4.1.0 h4f3a223_6 conda-forge
libwebp-base 1.1.0 h36c2ea0_3 conda-forge
lz4-c 1.9.2 he1b5a44_3 conda-forge
mafft 7.475 h516909a_0 bioconda
mash 1.1 0 bioconda
matplotlib-base 3.3.3 py39h98787fa_0 conda-forge
muscle 3.8.1551 hc9558a2_5 bioconda
ncurses 6.2 h58526e2_4 conda-forge
numpy 1.19.4 py39h57d35e7_1 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openssl 1.1.1h h516909a_0 conda-forge
pandas 1.1.5 py39hde0f152_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
perl-app-cpanminus 1.7044 pl526_1 bioconda
perl-archive-tar 2.32 pl526_0 bioconda
perl-base 2.23 pl526_1 bioconda
perl-business-isbn 3.004 pl526_0 bioconda
perl-business-isbn-data 20140910.003 pl526_0 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda
perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda
perl-constant 1.33 pl526_1 bioconda
perl-data-dumper 2.173 pl526_0 bioconda
perl-digest-hmac 1.03 pl526_3 bioconda
perl-digest-md5 2.55 pl526_0 bioconda
perl-encode 2.88 pl526_1 bioconda
perl-encode-locale 1.05 pl526_6 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.36 pl526_1 bioconda
perl-file-listing 6.04 pl526_1 bioconda
perl-file-path 2.16 pl526_0 bioconda
perl-file-temp 0.2304 pl526_2 bioconda
perl-html-parser 3.72 pl526h6bb024c_5 bioconda
perl-html-tagset 3.20 pl526_3 bioconda
perl-html-tree 5.07 pl526_1 bioconda
perl-http-cookies 6.04 pl526_0 bioconda
perl-http-daemon 6.01 pl526_1 bioconda
perl-http-date 6.02 pl526_3 bioconda
perl-http-message 6.18 pl526_0 bioconda
perl-http-negotiate 6.01 pl526_3 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-html 1.001 pl526_2 bioconda
perl-io-socket-ssl 2.066 pl526_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
perl-libwww-perl 6.39 pl526_0 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-lwp-mediatypes 6.04 pl526_0 bioconda
perl-lwp-protocol-https 6.07 pl526_4 bioconda
perl-mime-base64 3.15 pl526_1 bioconda
perl-mozilla-ca 20180117 pl526_1 bioconda
perl-net-http 6.19 pl526_0 bioconda
perl-net-ssleay 1.88 pl526h90d6eec_0 bioconda
perl-ntlm 1.09 pl526_4 bioconda
perl-parent 0.236 pl526_1 bioconda
perl-pathtools 3.75 pl526h14c3975_1 bioconda
perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda
perl-socket 2.027 pl526_1 bioconda
perl-storable 3.15 pl526h14c3975_0 bioconda
perl-test-requiresinternet 0.05 pl526_0 bioconda
perl-time-local 1.28 pl526_1 bioconda
perl-try-tiny 0.30 pl526_1 bioconda
perl-types-serialiser 1.0 pl526_2 bioconda
perl-uri 1.76 pl526_0 bioconda
perl-www-robotrules 6.02 pl526_3 bioconda
perl-xml-namespacesupport 1.12 pl526_0 bioconda
perl-xml-parser 2.44_01 pl526ha1d75be_1002 conda-forge
perl-xml-sax 1.02 pl526_0 bioconda
perl-xml-sax-base 1.09 pl526_0 bioconda
perl-xml-sax-expat 0.51 pl526_3 bioconda
perl-xml-simple 2.25 pl526_1 bioconda
perl-xsloader 0.24 pl526_0 bioconda
phylophlan 3.0.1 py_0 bioconda
pillow 8.0.1 py39h397ff4d_0 conda-forge
pip 20.3.1 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
python 3.9.1 hffdb5ce_0_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.9 1_cp39 conda-forge
pytz 2020.4 pyhd8ed1ab_0 conda-forge
raxml 8.2.12 h516909a_2 bioconda
readline 8.0 he28a2e2_2 conda-forge
scipy 1.5.3 py39hee8e79c_0 conda-forge
seaborn 0.11.0 ha770c72_1 conda-forge
seaborn-base 0.11.0 pyhd8ed1ab_1 conda-forge
setuptools 49.6.0 py39h079e4ff_2 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
sqlite 3.34.0 h74cdb3f_0 conda-forge
statsmodels 0.12.1 py39h16ac069_1 conda-forge
tk 8.6.10 hed695b0_1 conda-forge
tornado 6.1 py39hbd71b63_0 conda-forge
trimal 1.4.1 hc9558a2_4 bioconda
tzdata 2020d h516909a_0 conda-forge
wheel 0.36.1 pyhd3deb0d_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.4.5 h6597ccf_2 conda-forge

So perhaps the issue is that conda pulled the wrong version of fasttree from biocore?

Perhaps there could be a more specific yaml for PhyloPhlAn?

Thanks for these details.

Initially I thought there could have been a --force_nucleotides that would have break the -lg param in FastTree.

I’ve never tested FastTree from biocore, but I’ll test that to see if I can replicate your same issue.

The yaml for PhyloPhlAn is here https://github.com/biobakery/phylophlan/blob/master/recipe/meta.yaml, I could change the version to be >= 2.1.10 for FastTree in the next version.

Many thanks

I had the wrong version of FastTree for some reason, updating it helped :smile:

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