FastTreeMP returned non-zero exit status 1.

[gabridinosauro]

Hello phylophlan team,

Thanks for this cool tool!

I am trying to reconstruct the phylogenetic tree of some bins i receovered from metagenomes.
I am therefore running this command:

phylophlan -i /xdisk/laubitz/schiro/CPAE/clean/BIN_REASSEMBLY/reassembled_bins \
    -d phylophlan \
    --diversity high \
    -f /home/u1/schiro/phylo_plan/supermatrix_aa.cfg \
    --nproc 16 \
    --genome_extension .fa

Neverthtless I get this message of error:

Alignments concatenated "reassembled_bins_phylophlan/reassembled_bins_concatenated.aln" in 0s
Building phylogeny "reassembled_bins_phylophlan/reassembled_bins_concatenated.aln"

[e] Command '['/home/u1/schiro/.conda/envs/phylophlan/bin/FastTreeMP', '-quiet', '-pseudo', '-spr', '4', '-mlacc', '2', '-slownni', '-fastest', '-no2nd', '-mlnni', '4', '-lg', '-out', '/xdisk/laubitz/schiro/CPAE/clean/BIN_REASSEMBLY/phylophlan/reassembled_bins_phylophlan/reassembled_bins.tre', 'reassembled_bins_phylophlan/reassembled_bins_concatenated.aln']' returned non-zero exit status 1.

[e] error while executing
    command_line: /home/u1/schiro/.conda/envs/phylophlan/bin/FastTreeMP -quiet -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /xdisk/laubitz/schiro/CPAE/clean/BIN_REASSEMBLY/phylophlan/reassembled_bins_phylophlan/reassembled_bins.tre reassembled_bins_phylophlan/reassembled_bins_concatenated.aln
           stdin: None
          stdout: None

Any idea on how to help? thanks in advance for your awesome work!
Gabri

[fasnicar]

Hello Gabri,

Can you try running the FastTree command without the -quiet param

/home/u1/schiro/.conda/envs/phylophlan/bin/FastTreeMP -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /xdisk/laubitz/schiro/CPAE/clean/BIN_REASSEMBLY/phylophlan/reassembled_bins_phylophlan/reassembled_bins.tre reassembled_bins_phylophlan/reassembled_bins_concatenated.aln

so to better understand what's the problem?

Thanks a lot,
Francesco

[priscillaisaac98]

Hi,

I got the same error as @mrgambero where my command:

phylophlan -i /media/priscilla/Backup/Priscilla/Metawrap_binning_output/shotgun_total_MAGs_50_10 -d phylophlan --diversity low -f /home/priscilla/Documents/phylophlan_configuration_file/supermatrix_aa.cfg --output_folder /media/priscilla/Backup/Priscilla/phylophlan_output --genome_extension .fa

And this is the error that I get:

[e] Command '['/home/priscilla/anaconda3/envs/phylophlan/bin/FastTreeMP', '-quiet', '-pseudo', '-spr', '4', '-mlacc', '2', '-slownni', '-fastest', '-no2nd', '-mlnni', '4', '-lg', '-out', '/media/priscilla/Backup/Priscilla/phylophlan_output/shotgun_total_MAGs_50_10_phylophlan/shotgun_total_MAGs_50_10.tre', '/media/priscilla/Backup/Priscilla/phylophlan_output/shotgun_total_MAGs_50_10_phylophlan/shotgun_total_MAGs_50_10_concatenated.aln']' returned non-zero exit status 1.

[e] error while executing
command_line: /home/priscilla/anaconda3/envs/phylophlan/bin/FastTreeMP -quiet -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /media/priscilla/Backup/Priscilla/phylophlan_output/shotgun_total_MAGs_50_10_phylophlan/shotgun_total_MAGs_50_10.tre /media/priscilla/Backup/Priscilla/phylophlan_output/shotgun_total_MAGs_50_10_phylophlan/shotgun_total_MAGs_50_10_concatenated.aln
stdin: None
stdout: None

[nelsonruth11]

I am also having this error.

phylophlan \
    -i $input_genomes \
    -d phylophlan \
    -f $config_dir/supermatrix_aa.cfg \
    --diversity medium\
    --fast \
    -o $out_dir/$ref \
    --nproc 28

Which returns both of the errors described by the previous posters

[fasnicar]

To be able to understand the problem with FastTree, can you try running the FastTree command as printed in the error message and removing the -quiet param?

[ThomasYJK555]

To be able to understand the problem with FastTree, can you try running the FastTree command as printed in the error message and removing the -quiet param?

I have the same problem running with either iqtree or FastTree, even removing the "-quiet" didn't solve the problem.

[fasnicar]

Thanks @ThomasYJK555. The removal of the -quiet param was not meant to solve the problem, but instead to get a more informative output to be able to understand what's causing the problem with FastTree.
What's the output of FastTree when you re-ran it without the -quiet param?

Thanks,
Francesco

[mijiandui]

I am also having this error.

time phylophlan -i /home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_MAGs_ruminant_environment_50_drep0.99/dereplicated_genomes --genome_extension fa --diversity low -d phylophlan --fast --min_num_markers 1 --nproc 100 -f /home/yak/miniconda3/envs/phylophlan/lib/python3.11/site-packages/phylophlan/phylophlan_configs/supermatrix_aa.cfg -o /home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1 1>/home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1.log.txt 2>&1

the log file can be found in the attached document.
NC_meyhyl_50_227_phylophlan_fast_markers1.log.txt

Building phylogeny "/home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1/dereplicated_genomes_concatenated.aln"

[e] Command '['/home/yak/miniconda3/envs/phylophlan/bin/FastTreeMP', '-quiet', '-pseudo', '-spr', '4', '-mlacc', '2', '-slownni', '-fastest', '-no2nd', '-mlnni', '4', '-lg', '-out', '/home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1/dereplicated_genomes.tre', '/home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1/dereplicated_genomes_concatenated.aln']' returned non-zero exit status 1.

[e] error while executing
command_line: /home/yak/miniconda3/envs/phylophlan/bin/FastTreeMP -quiet -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1/dereplicated_genomes.tre /home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1/dereplicated_genomes_concatenated.aln
stdin: None
stdout: None
env: {'LESSOPEN': '| /usr/bin/lesspipe %s', 'CONDA_PROMPT_MODIFIER': '(phylophlan3.1.1) ', 'LANGUAGE': 'zh_CN:en', 'USER': 'yak', 'LC_TIME': 'zh_CN.UTF-8', 'XDG_SESSION_TYPE': 'x11', 'RCLONE_NO_CHECK_CERTIFICATE': 'true', 'SHLVL': '1', 'LD_LIBRARY_PATH': ':/opt/MonitorSoftware/lib:/usr/sfw/lib:/usr/local/lib', 'PERL_LOCAL_LIB_ROOT': '/home/yak/perl5', 'HOME': '/home/yak', 'CONDA_SHLVL': '1', 'OLDPWD': '/home/yak/NAS/nas', 'DESKTOP_SESSION': 'ubuntu', 'GNOME_SHELL_SESSION_MODE': 'ubuntu', 'GTK_MODULES': 'gail:atk-bridge', 'LC_MONETARY': 'zh_CN.UTF-8', 'SYSTEMD_EXEC_PID': '6687', 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1000/bus', 'COLORTERM': 'truecolor', 'CE_M': '', 'LOGNAME': 'yak', 'LIBPATH': ':/opt/MonitorSoftware/lib', '': '/home/yak/miniconda3/envs/phylophlan3.1.1/bin/phylophlan', 'XDG_SESSION_CLASS': 'user', 'USERNAME': 'yak', 'TERM': 'xterm-256color', 'PERL_MB_OPT': '--install_base "/home/yak/perl5"', 'GNOME_DESKTOP_SESSION_ID': 'this-is-deprecated', '_CE_CONDA': '', 'WINDOWPATH': '2', 'PATH': '/home/yak/miniconda3/envs/phylophlan3.1.1/bin:/home/yak/perl5/bin:/media/yak/Data/software/WIsH:/home/yak/miniconda3/envs/BASALT/bin:/usr/local/go/bin:/media/yak/Data/software/rclone-v1.55.1-linux-amd64:/media/yak/Data/metav/src:/home/yak/miniconda3/condabin:/home/yak/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin:/home/yak/edirect', 'SESSION_MANAGER': 'local/yak:@/tmp/.ICE-unix/4274,unix/yak:/tmp/.ICE-unix/4274', 'PAPERSIZE': 'a4', 'XDG_MENU_PREFIX': 'gnome-', 'LC_ADDRESS': 'zh_CN.UTF-8', 'GNOME_TERMINAL_SCREEN': '/org/gnome/Terminal/screen/4befa9f3_4de4_4391_894e_8492dd2fdf1f', 'PERL5LIB': '/home/yak/perl5/lib/perl5', 'XDG_RUNTIME_DIR': '/run/user/1000', 'DISPLAY': ':1', 'LANG': 'zh_CN.UTF-8', 'XDG_CURRENT_DESKTOP': 'ubuntu:GNOME', 'LC_TELEPHONE': 'zh_CN.UTF-8', 'XMODIFIERS': '@im=ibus', 'XDG_SESSION_DESKTOP': 'ubuntu', 'XAUTHORITY': '/run/user/1000/gdm/Xauthority', '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=00: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:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.zst=01;31:.tzst=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:.wim=01;31:.swm=01;31:.dwm=01;31:.esd=01;31:.jpg=01;35:.jpeg=01;35:.mjpg=01;35:.mjpeg=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:.webp=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:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36:', 'GNOME_TERMINAL_SERVICE': ':1.101', 'SSH_AGENT_LAUNCHER': 'gnome-keyring', 'SSH_AUTH_SOCK': '/run/user/1000/keyring/ssh', 'CONDA_PYTHON_EXE': '/home/yak/miniconda3/bin/python', 'SHELL': '/bin/bash', 'LC_NAME': 'zh_CN.UTF-8', 'SHLIB_PATH': ':/opt/MonitorSoftware/lib', 'QT_ACCESSIBILITY': '1', 'GDMSESSION': 'ubuntu', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'PERL_MM_OPT': 'INSTALL_BASE=/home/yak/perl5', 'CONDA_DEFAULT_ENV': 'phylophlan3.1.1', 'LC_MEASUREMENT': 'zh_CN.UTF-8', 'GPG_AGENT_INFO': '/run/user/1000/gnupg/S.gpg-agent:0:1', 'LC_IDENTIFICATION': 'zh_CN.UTF-8', 'QT_IM_MODULE': 'ibus', 'PWD': '/home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_MAGs_ruminant_environment_50', 'LC_ALL': 'en_US.UTF-8', 'XDG_CONFIG_DIRS': '/etc/xdg/xdg-ubuntu:/etc/xdg', 'CONDA_EXE': '/home/yak/miniconda3/bin/conda', 'XDG_DATA_DIRS': '/usr/share/ubuntu:/usr/share/gnome:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop', 'LC_NUMERIC': 'zh_CN.UTF-8', 'CONDA_PREFIX': '/home/yak/miniconda3/envs/phylophlan3.1.1', 'LC_PAPER': 'zh_CN.UTF-8', 'VTE_VERSION': '6800', 'OMP_NUM_THREADS': '3'}

[mijiandui]

when we run solely:

/home/yak/miniconda3/envs/phylophlan/bin/FastTreeMP -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1/dereplicated_genomes.tre /home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1/dereplicated_genomes_concatenated.aln

the error information as following:

FastTree Version 2.1.11 Double precision (No SSE3), OpenMP (112 threads)
Alignment: /home/yak/NAS/nas/ruminant_archaea_all_culture0.99/NC_meyhyl_50_227_phylophlan_fast_markers1/dereplicated_genomes_concatenated.aln
Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search: Fastest +NNI +SPR (4 rounds range 10) +ML-NNI (4 rounds) opt-each=2
TopHits: 1.00*sqrtN close=default refresh=0.50
ML Model: Le-Gascuel 2008, CAT approximation with 20 rate categories
Pseudocount weight for comparing sequences with little overlap: 1.000
Wrong number of characters for GCA_017626935.1_ASM1762693v1_genomic: expected 44940 but have 36203 instead.
This sequence may be truncated, or another sequence may be too long.