Phylophlan error after generating the concatenated alignment

Microbial community profiling PhyloPhlAn
1

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’, ‘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!

2

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)

/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