# Error running FastTreeMP step

**URL:** <https://forum.biobakery.org/t/error-running-fasttreemp-step/1413>\
**Category:** PhyloPhlAn\
**Created:** [December 8, 2020, 9:51pm UTC](https://forum.biobakery.org/t/error-running-fasttreemp-step/1413 "2020-12-08T21:51:42Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![BioMickWatson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/biomickwatson/32/359_2.png) [@BioMickWatson](https://forum.biobakery.org/u/BioMickWatson)\
**Post date:** [December 8, 2020, 9:51pm UTC](https://forum.biobakery.org/t/error-running-fasttreemp-step/1413/1 "2020-12-08T21:51:42Z")

</div>

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](http://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?

---

<div class="post-metadata">

**Author:** ![BioMickWatson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/biomickwatson/32/359_2.png) [@BioMickWatson](https://forum.biobakery.org/u/BioMickWatson)\
**Post date:** [December 8, 2020, 10:03pm UTC](https://forum.biobakery.org/t/error-running-fasttreemp-step/1413/2 "2020-12-08T22:03:12Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\
**Post date:** [December 9, 2020, 10:16am UTC](https://forum.biobakery.org/t/error-running-fasttreemp-step/1413/3 "2020-12-09T10:16:05Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![BioMickWatson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/biomickwatson/32/359_2.png) [@BioMickWatson](https://forum.biobakery.org/u/BioMickWatson)\
**Post date:** [December 9, 2020, 10:57am UTC](https://forum.biobakery.org/t/error-running-fasttreemp-step/1413/4 "2020-12-09T10:57:17Z")

</div>

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?

---

<div class="post-metadata">

**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\
**Post date:** [December 9, 2020, 1:53pm UTC](https://forum.biobakery.org/t/error-running-fasttreemp-step/1413/5 "2020-12-09T13:53:27Z")

</div>

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](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

---

<div class="post-metadata">

**Author:** ![BioMickWatson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/biomickwatson/32/359_2.png) [@BioMickWatson](https://forum.biobakery.org/u/BioMickWatson)\
**Post date:** [January 21, 2021, 3:12pm UTC](https://forum.biobakery.org/t/error-running-fasttreemp-step/1413/6 "2021-01-21T15:12:49Z")

</div>

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