# Phylophlan error after generating the concatenated alignment

**URL:** <https://forum.biobakery.org/t/phylophlan-error-after-generating-the-concatenated-alignment/4881>\
**Category:** PhyloPhlAn\
**Created:** [March 1, 2023, 4:10am UTC](https://forum.biobakery.org/t/phylophlan-error-after-generating-the-concatenated-alignment/4881 "2023-03-01T04:10:40Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![saras22](https://avatars.discourse-cdn.com/v4/letter/s/59ef9b/32.png) [@saras22](https://forum.biobakery.org/u/saras22)\
**Post date:** [March 1, 2023, 4:10am UTC](https://forum.biobakery.org/t/phylophlan-error-after-generating-the-concatenated-alignment/4881/1 "2023-03-01T04:10:40Z")

</div>

phylophlan error after generating the concatenated alignment

Command that I used:  
phylophlan --input /home/rakesh/MAIN\_DREPOUT\_ABOVE\_50\_ANI99\_NC0.3\_con\_10/DREP\_CON5\_COMP90\_BINS/GTDB/Prevelent\_bin\_species/Moraxella/ -d phylophlan -t a --databases\_folder /home/rakesh/PHYLO\_ANALYSIS/PHYLO\_DB/ --diversity low --output\_folder /home/rakesh/MAIN\_DREPOUT\_ABOVE\_50\_ANI99\_NC0.3\_con\_10/DREP\_CON5\_COMP90\_BINS/GTDB/Prevelent\_bin\_species/Moraxella/PHYLO\_TREE/ -f /home/rakesh/PHYLO\_ANALYSIS/PHYLO\_OUT2/supermatrix\_aa.cfg --genome\_extension .fasta --nproc 12

error after making concatenated.aln file

[e] Command ‘[’/home/rsharma/anaconda3/bin/FastTreeMP’, ‘-quiet’, ‘-pseudo’, ‘-spr’, ‘4’, ‘-mlacc’, ‘2’, ‘-slownni’, ‘-fastest’, ‘-no2nd’, ‘-mlnni’, ‘4’, ‘-lg’, ‘-out’, ‘/lustre/rsharma/MAIN\_DREPOUT\_ABOVE\_50\_ANI99\_NC0.3\_con\_10/ABRICATE\_PATH/E\_coli\_bins/PHYLO\_OUT1/IN\_phylophlan/IN.tre’, ‘/lustre/rsharma/MAIN\_DREPOUT\_ABOVE\_50\_ANI99\_NC0.3\_con\_10/ABRICATE\_PATH/E\_coli\_bins/PHYLO\_OUT1/IN\_phylophlan/IN\_concatenated.aln’]’ returned non-zero exit status 1.

[e] error while executing  
command\_line: /home/rsharma/anaconda3/bin/FastTreeMP -quiet -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /lustre/rsharma/MAIN\_DREPOUT\_ABOVE\_50\_ANI99\_NC0.3\_con\_10/ABRICATE\_PATH/E\_coli\_bins/PHYLO\_OUT1/IN\_phylophlan/IN.tre /lustre/rsharma/MAIN\_DREPOUT\_ABOVE\_50\_ANI99\_NC0.3\_con\_10/ABRICATE\_PATH/E\_coli\_bins/PHYLO\_OUT1/IN\_phylophlan/IN\_concatenated.aln  
stdin: None  
stdout: None  
env: {‘SLURM\_NODELIST’: ‘smp1’, ‘CONGO\_PORT’: ‘12430’, ‘CONGO\_URL’: ‘[http://127.0.0.1:12429](http://127.0.0.1:12429)’, ‘AS’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-as’, ‘SLURM\_JOB\_NAME’: ‘path\_phylo’, ‘MANPATH’: ‘/lustre/apps/ompi4.1/share/man:/lustre/apps/gcc-8.4/share:/opt/xcat/share/man:/opt/xcat/share/man:’, ‘CONGO\_SERVER\_HOST’: ‘127.0.0.1’, ‘AR’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-ar’, ‘LDFLAGS’: ‘-Wl,-O2 -Wl,–sort-common -Wl,–as-needed -Wl,-z,relro -Wl,-z,now -Wl,–disable-new-dtags -Wl,–gc-sections -Wl,-rpath,/home/rsharma/anaconda3/lib -Wl,-rpath-link,/home/rsharma/anaconda3/lib -L/home/rsharma/anaconda3/lib’, ‘XDG\_SESSION\_ID’: ‘8011’, ‘SLURMD\_NODENAME’: ‘smp1’, ‘SLURM\_TOPOLOGY\_ADDR’: ‘smp1’, ‘SLURM\_NTASKS\_PER\_NODE’: ‘80’, ‘HOSTNAME’: ‘smp1’, ‘GCC\_NM’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-gcc-nm’, ‘JAVA\_LD\_LIBRARY\_PATH’: ‘/home/rsharma/anaconda3/lib/server’, ‘SLURM\_PRIO\_PROCESS’: ‘0’, ‘SLURM\_NODE\_ALIASES’: ‘(null)’, ‘CGE\_RESFINDER\_RESGENE\_DB’: ‘/lustre/rsharma/resfinder\_db’, ‘HOST’: ‘x86\_64-conda\_cos6-linux-gnu’, ‘TERM’: ‘xterm-256color’, ‘SHELL’: ‘/bin/bash’, ‘SLURM\_JOB\_QOS’: ‘normal’, ‘HISTSIZE’: ‘1000’, ‘NM’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-nm’, ‘TMPDIR’: ‘/tmp’, ‘SLURM\_TOPOLOGY\_ADDR\_PATTERN’: ‘node’, ‘SSH\_CLIENT’: ‘192.168.13.59 33996 22’, ‘CPPFLAGS’: ‘-DNDEBUG -D\_FORTIFY\_SOURCE=2 -O2 -isystem /home/rsharma/anaconda3/include’, ‘LIBRARY\_PATH’: ‘/lustre/apps/ompi4.1/lib’, ‘PERL5LIB’: ‘/home/rsharma/perl5/lib/perl5:/home/rsharma/perl5/lib/perl5’, ‘CONDA\_SHLVL’: ‘1’, ‘CONDA\_PROMPT\_MODIFIER’: '(base) ', ‘FPATH’: ‘/lustre/apps/ompi4.1/include’, ‘SIZE’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-size’, ‘PERL\_MB\_OPT’: ‘–install\_base “/home/rsharma/perl5”’, ‘INCLUDE\_PATH’: ‘/lustre/apps/ompi4.1/include’, ‘SSH\_TTY’: ‘/dev/pts/44’, ‘PERL\_BADLANG’: ‘0’, ‘SLURM\_NNODES’: ‘1’, ‘USER’: ‘rsharma’, ‘LS\_COLORS’: ‘rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:_.tar=38;5;9:_.tgz=38;5;9:_.arc=38;5;9:_.arj=38;5;9:_.taz=38;5;9:_.lha=38;5;9:_.lz4=38;5;9:_.lzh=38;5;9:_.lzma=38;5;9:_.tlz=38;5;9:_.txz=38;5;9:_.tzo=38;5;9:_.t7z=38;5;9:_.zip=38;5;9:_.z=38;5;9:_.Z=38;5;9:_.dz=38;5;9:_.gz=38;5;9:_.lrz=38;5;9:_.lz=38;5;9:_.lzo=38;5;9:_.xz=38;5;9:_.bz2=38;5;9:_.bz=38;5;9:_.tbz=38;5;9:_.tbz2=38;5;9:_.tz=38;5;9:_.deb=38;5;9:_.rpm=38;5;9:_.jar=38;5;9:_.war=38;5;9:_.ear=38;5;9:_.sar=38;5;9:_.rar=38;5;9:_.alz=38;5;9:_.ace=38;5;9:_.zoo=38;5;9:_.cpio=38;5;9:_.7z=38;5;9:_.rz=38;5;9:_.cab=38;5;9:_.jpg=38;5;13:_.jpeg=38;5;13:_.gif=38;5;13:_.bmp=38;5;13:_.pbm=38;5;13:_.pgm=38;5;13:_.ppm=38;5;13:_.tga=38;5;13:_.xbm=38;5;13:_.xpm=38;5;13:_.tif=38;5;13:_.tiff=38;5;13:_.png=38;5;13:_.svg=38;5;13:_.svgz=38;5;13:_.mng=38;5;13:_.pcx=38;5;13:_.mov=38;5;13:_.mpg=38;5;13:_.mpeg=38;5;13:_.m2v=38;5;13:_.mkv=38;5;13:_.webm=38;5;13:_.ogm=38;5;13:_.mp4=38;5;13:_.m4v=38;5;13:_.mp4v=38;5;13:_.vob=38;5;13:_.qt=38;5;13:_.nuv=38;5;13:_.wmv=38;5;13:_.asf=38;5;13:_.rm=38;5;13:_.rmvb=38;5;13:_.flc=38;5;13:_.avi=38;5;13:_.fli=38;5;13:_.flv=38;5;13:_.gl=38;5;13:_.dl=38;5;13:_.xcf=38;5;13:_.xwd=38;5;13:_.yuv=38;5;13:_.cgm=38;5;13:_.emf=38;5;13:_.axv=38;5;13:_.anx=38;5;13:_.ogv=38;5;13:_.ogx=38;5;13:_.aac=38;5;45:_.au=38;5;45:_.flac=38;5;45:_.mid=38;5;45:_.midi=38;5;45:_.mka=38;5;45:_.mp3=38;5;45:_.mpc=38;5;45:_.ogg=38;5;45:_.ra=38;5;45:_.wav=38;5;45:_.axa=38;5;45:_.oga=38;5;45:_.spx=38;5;45:\*.xspf=38;5;45:’, ‘LD\_LIBRARY\_PATH’: ‘/lustre/apps/ompi4.1/lib:/lustre/apps/gcc-8.4/lib64:/lustre/apps/gcc-8.4/lib’, ‘CONDA\_BACKUP\_HOST’: ‘x86\_64-conda\_cos6-linux-gnu’, ‘CGE\_DISINFINDER\_DB’: ‘/lustre/rsharma/disinfinder\_db’, ‘CGE\_RESFINDER\_RESPOINT\_DB’: ‘/lustre/rsharma/pointfinder\_db’, ‘CONDA\_EXE’: ‘/home/rsharma/anaconda3/bin/conda’, ‘XCATROOT’: ‘/opt/xcat’, ‘SLURM\_JOBID’: ‘43452’, ‘CPATH’: ‘/lustre/apps/ompi4.1/include:/lustre/apps/gcc-8.4/include’, ‘SLURM\_NTASKS’: ‘80’, ‘CXXFLAGS’: ‘-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rsharma/anaconda3/include’, ‘LD\_GOLD’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-ld.gold’, ‘STRINGS’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-strings’, ‘CONDA\_BUILD\_SYSROOT’: ‘/home/rsharma/anaconda3/x86\_64-conda\_cos6-linux-gnu/sysroot’, ‘\_CE\_CONDA’: ‘’, ‘CPP’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-cpp’, ‘CONGO\_CONSOLE\_TIMEOUT’: ‘3’, ‘CXXFILT’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-c++filt’, ‘SLURM\_TASKS\_PER\_NODE’: ‘80’, ‘MAIL’: ‘/var/spool/mail/rsharma’, ‘PATH’: ‘/lustre/apps/ompi4.1/bin:/home/rsharma/phylophlan/phylophlan:/home/rsharma/KRAKEN2\_DIR:/home/rsharma/KRAKEN2\_DIR/bin:/home/rsharma/perl5/bin:/lustre/rsharma/singularity/go/bin://lustre/rsharma/singularity-run/bin:/lustre/apps/gcc-8.4/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/share/xcat/tools:/lustre/apps/go/bin:/lustre/apps/singularity/3.7.4/bin:/opt/slurm/bin:/home/rsharma/phylophlan/phylophlan:/home/rsharma/KRAKEN2\_DIR:/home/rsharma/KRAKEN2\_DIR/bin:/home/rsharma/perl5/bin:/lustre/rsharma/singularity/go/bin://lustre/rsharma/singularity-run/bin:/home/rsharma/anaconda3/bin:/home/rsharma/anaconda3/condabin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/share/xcat/tools:/lustre/apps/go/bin:/lustre/apps/singularity/3.7.4/bin:/opt/slurm/bin:/usr/local/bin:/usr/bin:/opt/ibutils/bin:/lustre/rsharma/MetaWRAP/bin:/usr/local/sbin:/usr/sbin:/lustre/rsharma/MetaWRAP/bin/:/home/rsharma/bin’, ‘SLURM\_WORKING\_CLUSTER’: ‘tejas-cluster:hn1:6817:9216:101’, ‘SLURM\_CONF’: ‘/etc/slurm/slurm.conf’, ‘CONGO\_SSL\_INSECURE’: ‘false’, ‘SLURM\_JOB\_ID’: ‘43452’, ‘CONDA\_PREFIX’: ‘/home/rsharma/anaconda3’, ‘LD’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-ld’, ‘DEBUG\_CXXFLAGS’: ‘-fvisibility-inlines-hidden -std=c++17 -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/rsharma/anaconda3/include’, ‘SLURM\_JOB\_USER’: ‘rsharma’, ‘PWD’: ‘/home/rsharma/lustre/MAIN\_DREPOUT\_ABOVE\_50\_ANI99\_NC0.3\_con\_10/ABRICATE\_PATH/E\_coli\_bins’, ‘PDSH\_RCMD\_TYPE’: ‘ssh’, ‘_LMFILES_’: ‘/lustre/module/modulefiles/gcc-8.4:/lustre/module/modulefiles/openmpi-4.1’, ‘STRIP’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-strip’, ‘JAVA\_HOME’: ‘/home/rsharma/anaconda3’, ‘ELFEDIT’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-elfedit’, ‘LANG’: ‘C.UTF-8’, ‘GCC\_RANLIB’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-gcc-ranlib’, ‘MODULEPATH’: ‘/etc/modulefiles:/lustre/module/modulefiles’, ‘SLURM\_JOB\_UID’: ‘30649’, ‘LOADEDMODULES’: ‘gcc-8.4:openmpi-4.1’, ‘SLURM\_NODEID’: ‘0’, ‘GTDBTK\_DATA\_PATH’: ‘/lustre/rsharma/release207\_v2/’, ‘SLURM\_SUBMIT\_DIR’: ‘/lustre/rsharma/MAIN\_DREPOUT\_ABOVE\_50\_ANI99\_NC0.3\_con\_10/ABRICATE\_PATH/E\_coli\_bins’, ‘SLURM\_TASK\_PID’: ‘89384’, ‘SLURM\_NPROCS’: ‘80’, ‘SLURM\_CPUS\_ON\_NODE’: ‘80’, ‘SLURM\_PROCID’: ‘0’, ‘ENVIRONMENT’: ‘BATCH’, ‘\_CE\_M’: ‘’, ‘HISTCONTROL’: ‘ignoredups’, ‘CXX’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-c++’, ‘SLURM\_JOB\_NODELIST’: ‘smp1’, ‘KRAKEN\_PATH’: ‘/home/rsharma/KRAKEN2\_DIR/kraken2-master’, ‘OBJCOPY’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-objcopy’, ‘SHLVL’: ‘2’, ‘HOME’: ‘/home/rsharma’, ‘WCOLL’: ‘/etc/machinefile’, ‘SLURM\_LOCALID’: ‘0’, ‘SLURM\_JOB\_GID’: ‘30660’, ‘SLURM\_JOB\_CPUS\_PER\_NODE’: ‘80’, ‘SLURM\_CLUSTER\_NAME’: ‘tejas-cluster’, ‘CFLAGS’: ‘-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/rsharma/anaconda3/include’, ‘DEBUG\_CPPFLAGS’: ‘-D\_DEBUG -D\_FORTIFY\_SOURCE=2 -Og -isystem /home/rsharma/anaconda3/include’, ‘SLURM\_GTIDS’: ‘0’, ‘SLURM\_SUBMIT\_HOST’: ‘hn1.dc’, ‘GCC’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-gcc’, ‘\_CONDA\_PYTHON\_SYSCONFIGDATA\_NAME’: ‘_sysconfigdata\_x86\_64\_conda\_cos6\_linux\_gnu’, ‘SLURM\_JOB\_PARTITION’: ‘smp’, ‘PERL\_LOCAL\_LIB\_ROOT’: ‘/home/rsharma/perl5:/home/rsharma/perl5’, ‘CONDA\_PYTHON\_EXE’: ‘/home/rsharma/anaconda3/bin/python’, ‘LOGNAME’: ‘rsharma’, ‘ADDR2LINE’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-addr2line’, ‘XDG\_DATA\_DIRS’: ‘/home/rsharma/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share’, ‘SSH\_CONNECTION’: ‘192.168.13.59 33996 192.168.25.13 22’, ‘SLURM\_JOB\_NUM\_NODES’: ‘1’, ‘MODULESHOME’: ‘/lustre/apps/gcc-8.4’, ‘PKG\_CONFIG\_PATH’: ‘/lustre/apps/ompi4.1/lib/pkgconfig’, ‘CONDA\_DEFAULT\_ENV’: ‘base’, ‘GOPATH’: ‘/lustre/rsharma/singularity/go’, ‘LESSOPEN’: ‘||/usr/bin/lesspipe.sh %s’, ‘JAVA\_HOME\_CONDA\_BACKUP’: ‘’, ‘RANLIB’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-ranlib’, ‘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/rsharma/anaconda3/include’, ‘XDG\_RUNTIME\_DIR’: ‘/run/user/30649’, ‘CC’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-cc’, ‘CMAKE\_PREFIX\_PATH’: ‘/home/rsharma/anaconda3:/home/rsharma/anaconda3/x86\_64-conda\_cos6-linux-gnu/sysroot/usr’, ‘READELF’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-readelf’, ‘JAVA\_LD\_LIBRARY\_PATH\_BACKUP’: ‘’, ‘OBJDUMP’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-objdump’, ‘GCC\_AR’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-gcc-ar’, ‘PERL\_MM\_OPT’: ‘INSTALL\_BASE=/home/rsharma/perl5’, ‘GPROF’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-gprof’, ‘GXX’: ‘/home/rsharma/anaconda3/bin/x86\_64-conda\_cos6-linux-gnu-g++’, ‘BASH\_FUNC\_module()’: ‘() { eval `/usr/bin/modulecmd bash $*`\n}’, '_’: ‘/home/rsharma/anaconda3/bin/phylophlan’, ‘OMP\_NUM\_THREADS’: ‘3’}

Please let me know what is the issue so that I can resolve it?

Thanks in Advance!

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<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:** [March 20, 2023, 9:19pm UTC](https://forum.biobakery.org/t/phylophlan-error-after-generating-the-concatenated-alignment/4881/2 "2023-03-20T21:19:32Z")

</div>

Hi there,

have you / can you try tunning the FastTree command from the error message?  
(I just got rid of the `-quiet` param to get some more output info)

```auto
/home/rsharma/anaconda3/bin/FastTreeMP -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /lustre/rsharma/MAIN_DREPOUT_ABOVE_50_ANI99_NC0.3_con_10/ABRICATE_PATH/E_coli_bins/PHYLO_OUT1/IN_phylophlan/IN.tre /lustre/rsharma/MAIN_DREPOUT_ABOVE_50_ANI99_NC0.3_con_10/ABRICATE_PATH/E_coli_bins/PHYLO_OUT1/IN_phylophlan/IN_concatenated.aln

```

Thanks a lot,  
Francesco