FastTreeMP execution error

Microbial community profiling PhyloPhlAn
1

Hi there.
Iwas wondering if I could get some help on this error I’m getting. I’ve run phylophal version 3.1.68, installed in a separate environment. the fir 2 runs were succesfull and now for my other MAGs and their coresponding reference bugs, I’m getting this error:

[e] Command ‘[’/home/aam2195/.conda/envs/phylophlan/bin/FastTreeMP’, ‘-quiet’, ‘-pseudo’, ‘-spr’, ‘4’, ‘-mlacc’, ‘2’, ‘-slownni’, ‘-fastest’, ‘-no2nd’, ‘-mlnni’, ‘4’, ‘-lg’, ‘-out’, ‘/gpfs/projects/b1042/HartmannLab/Howler/phylophlan/output_Roseburia/Roseburia.tre’, ‘output_Roseburia/Roseburia_concatenated.aln’]’ returned non-zero exit status 1.

[e] error while executing
command_line: /home/aam2195/.conda/envs/phylophlan/bin/FastTreeMP -quiet -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /gpfs/projects/b1042/HartmannLab/Howler/phylophlan/output_Roseburia/Roseburia.tre output_Roseburia/Roseburia_concatenated.aln
stdin: None
stdout: None
env: {‘HYDRA_LAUNCHER_EXTRA_ARGS’: ‘–external-launcher’, ‘CONDA_SHLVL’: ‘2’, ‘LS_COLORS’: ‘rs=0:di=38;5;33:ln=38;5;51:mh=00: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=01;05;37;41: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;40:.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:.dz=38;5;9:.gz=38;5;9:.lrz=38;5;9:.lz=38;5;9:.lzo=38;5;9:.xz=38;5;9:.zst=38;5;9:.tzst=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:.wim=38;5;9:.swm=38;5;9:.dwm=38;5;9:.esd=38;5;9:.jpg=38;5;13:.jpeg=38;5;13:.mjpg=38;5;13:.mjpeg=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:.ogv=38;5;13:.ogx=38;5;13:.aac=38;5;45:.au=38;5;45:.flac=38;5;45:.m4a=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:.oga=38;5;45:.opus=38;5;45:.spx=38;5;45:.xspf=38;5;45:', ‘CONDA_EXE’: ‘/software/miniconda3/mamba-0.15.3/bin/conda’, ‘SLURM_NODEID’: ‘0’, ‘SLURM_TASK_PID’: ‘3711795’, ‘__LMOD_REF_COUNT_PATH’: ‘/software/FastTreeMP/2.1.10:1;/gpfs/home/aam2195/.vscode-server/bin/0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2/bin/remote-cli:1;/home/aam2195/.conda/envs/phylophlan/bin:1;/software/miniconda3/mamba-0.15.3/condabin:1;/usr/local/bin:1;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;/usr/lpp/mmfs/bin:3;/hpc/usertools:3’, ‘ModuleTable002’: ‘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’, ‘SSH_CONNECTION’: ‘129.105.9.98 51281 165.124.130.51 22’, ‘SLURM_PRIO_PROCESS’: ‘0’, ‘_’: ‘/home/aam2195/.conda/envs/phylophlan/bin/phylophlan’, ‘I_MPI_HYDRA_BOOTSTRAP_EXEC_EXTRA_ARGS’: ‘–external-launcher’, ‘LANG’: ‘en_US.UTF-8’, ‘SLURM_SUBMIT_DIR’: ‘/gpfs/projects/b1042/HartmannLab/Howler/phylophlan’, ‘HISTCONTROL’: ‘ignoredups’, ‘OMPI_MCA_plm_slurm_args’: ‘–external-launcher’, ‘HOSTNAME’: ‘qnode1266’, ‘OLDPWD’: ‘/projects/b1042/HartmannLab/Howler/phylophlan’, ‘ENVIRONMENT’: ‘BATCH’, ‘COLORTERM’: ‘truecolor’, ‘CONDA_PREFIX’: ‘/home/aam2195/.conda/envs/phylophlan’, ‘VSCODE_GIT_ASKPASS_EXTRA_ARGS’: ‘’, ‘SLURM_PROCID’: ‘0’, ‘SLURM_JOB_GID’: ‘4952’, ‘I_MPI_HYDRA_BOOTSTRAP’: ‘slurm’, ‘SLURMD_NODENAME’: ‘qnode1266’, ‘SLURM_JOB_END_TIME’: ‘1754353023’, ‘SLURM_TASKS_PER_NODE’: ‘16’, ‘PRTE_MCA_plm_slurm_args’: ‘–external-launcher’, ‘_CE_M’: ‘’, ‘which_declare’: ‘declare -f’, ‘XDG_SESSION_ID’: ‘263909’, ‘USER’: ‘aam2195’, ‘SLURM_NNODES’: ‘1’, ‘CONDA_PREFIX_1’: ‘/software/miniconda3/mamba-0.15.3’, ‘SLURM_JOB_START_TIME’: ‘1754338623’, ‘__LMOD_REF_COUNT_MODULEPATH’: ‘/hpc/software/Modules/3.2.9/modulefiles:1;/hpc/software/Modules/3.2.9/deprecated:1;/hpc/software/Modules/spack-modules/linux-rhel7-x86_64:1;/hpc/software/spack_v20d1/spack/share/spack/modules/linux-rhel7-x86_64:1;/hpc/software/spack_v17d2/spack/share/spack/modules/linux-rhel7-x86_64:1;/hpc/software/2025/spack/share/spack/modules/linux-rhel8-x86_64:1’, ‘PWD’: ‘/projects/b1042/HartmannLab/Howler/phylophlan’, ‘SLURM_JOB_NODELIST’: ‘qnode1266’, ‘HOME’: ‘/home/aam2195’, ‘SLURM_CLUSTER_NAME’: ‘quest’, ‘CONDA_PYTHON_EXE’: ‘/software/miniconda3/mamba-0.15.3/bin/python’, ‘BROWSER’: ‘/gpfs/home/aam2195/.vscode-server/bin/0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2/bin/helpers/browser.sh’, ‘VSCODE_GIT_ASKPASS_NODE’: ‘/gpfs/home/aam2195/.vscode-server/bin/0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2/node’, ‘SLURM_NODELIST’: ‘qnode1266’, ‘TERM_PROGRAM’: ‘vscode’, ‘SSH_CLIENT’: ‘129.105.9.98 51281 22’, ‘TERM_PROGRAM_VERSION’: ‘1.85.1’, ‘LMOD_VERSION’: ‘8.7.24’, ‘SLURM_NTASKS’: ‘16’, ‘KRB5CCNAME’: ‘KCM:’, ‘SLURM_JOB_CPUS_PER_NODE’: ‘16’, ‘BASH_ENV’: ‘/hpc/software/spack_v20d1/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lmod-8.7.24-ptfr7cudrme2v7y2nfktkkftnrgkezra/lmod/lmod/init/bash’, ‘XDG_DATA_DIRS’: ‘/home/aam2195/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share’, ‘SLURM_TOPOLOGY_ADDR’: ‘qnode1266’, ‘_CE_CONDA’: ‘’, ‘VSCODE_IPC_HOOK_CLI’: ‘/tmp/vscode-ipc-0c8fdecc-3d46-4d38-8949-2f3f6c6af617.sock’, ‘SLURM_JOB_NAME’: ‘phylophlan’, ‘TMPDIR’: ‘/tmp’, ‘LMOD_sys’: ‘Linux’, ‘SLURM_JOBID’: ‘791928’, ‘ModuleTable001’: ‘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’, ‘SLURM_CONF’: ‘/etc/slurm/slurm.conf’, ‘LOADEDMODULES’: ‘FastTreeMP/2.1.10’, ‘LMOD_AVAIL_STYLE’: ‘en_grouped:system’, ‘ModuleTable003’: ‘L3NvZnR3YXJlL01vZHVsZXMvMy4yLjkvbW9kdWxlZmlsZXM6L2hwYy9zb2Z0d2FyZS9Nb2R1bGVzLzMuMi45L2RlcHJlY2F0ZWQ6L2hwYy9zb2Z0d2FyZS9Nb2R1bGVzL3NwYWNrLW1vZHVsZXMvbGludXgtcmhlbDcteDg2XzY0Oi9ocGMvc29mdHdhcmUvc3BhY2tfdjIwZDEvc3BhY2svc2hhcmUvc3BhY2svbW9kdWxlcy9saW51eC1yaGVsNy14ODZfNjQ6L2hwYy9zb2Z0d2FyZS9zcGFja192MTdkMi9zcGFjay9zaGFyZS9zcGFjay9tb2R1bGVzL2xpbnV4LXJoZWw3LXg4Nl82NDovaHBjL3NvZnR3YXJlLzIwMjUvc3BhY2svc2hhcmUvc3BhY2svbW9kdWxlcy9saW51eC1yaGVsOC14ODZfNjQiLAp9Cg==’, ‘LMOD_ROOT’: ‘/hpc/software/spack_v20d1/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lmod-8.7.24-ptfr7cudrme2v7y2nfktkkftnrgkezra/lmod’, ‘SLURM_JOB_QOS’: ‘normal’, ‘SLURM_TOPOLOGY_ADDR_PATTERN’: ‘node’, ‘CONDA_PROMPT_MODIFIER’: '(phylophlan) ', ‘MAIL’: ‘/var/spool/mail/aam2195’, ‘SLURM_CPUS_ON_NODE’: ‘16’, ‘VSCODE_GIT_ASKPASS_MAIN’: ‘/gpfs/home/aam2195/.vscode-server/bin/0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2/extensions/git/dist/askpass-main.js’, ‘SLURM_JOB_NUM_NODES’: ‘1’, ‘TERM’: ‘xterm-256color’, ‘SHELL’: ‘/bin/bash’, ‘SLURM_JOB_UID’: ‘4286’, ‘ModuleTable_Sz’: ‘3’, ‘SLURM_JOB_PARTITION’: ‘short’, ‘SLURM_JOB_USER’: ‘aam2195’, ‘SLURM_NPROCS’: ‘16’, ‘SHLVL’: ‘6’, ‘SLURM_SUBMIT_HOST’: ‘quser41’, ‘VSCODE_GIT_IPC_HANDLE’: ‘/tmp/vscode-git-d9fb98cbc8.sock’, ‘SLURM_JOB_ACCOUNT’: ‘p32045’, ‘MANPATH’: ‘/hpc/software/spack_v20d1/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lmod-8.7.24-ptfr7cudrme2v7y2nfktkkftnrgkezra/lmod/lmod/share/man:’, ‘HYDRA_BOOTSTRAP’: ‘slurm’, ‘MODULEPATH’: ‘/hpc/software/Modules/3.2.9/modulefiles:/hpc/software/Modules/3.2.9/deprecated:/hpc/software/Modules/spack-modules/linux-rhel7-x86_64:/hpc/software/spack_v20d1/spack/share/spack/modules/linux-rhel7-x86_64:/hpc/software/spack_v17d2/spack/share/spack/modules/linux-rhel7-x86_64:/hpc/software/2025/spack/share/spack/modules/linux-rhel8-x86_64’, ‘SLURM_GTIDS’: ‘0’, ‘LOGNAME’: ‘aam2195’, ‘DBUS_SESSION_BUS_ADDRESS’: ‘unix:path=/run/user/4286/bus’, ‘GIT_ASKPASS’: ‘/gpfs/home/aam2195/.vscode-server/bin/0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2/extensions/git/dist/askpass.sh’, ‘MODULEPATH_ROOT’: ‘/hpc/software/spack_v20d1/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lmod-8.7.24-ptfr7cudrme2v7y2nfktkkftnrgkezra/modulefiles’, ‘PATH’: ‘/software/FastTreeMP/2.1.10:/gpfs/home/aam2195/.vscode-server/bin/0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2/bin/remote-cli:/home/aam2195/.conda/envs/phylophlan/bin:/software/miniconda3/mamba-0.15.3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/hpc/usertools’, ‘SLURM_JOB_ID’: ‘791928’, ‘LMFILES’: ‘/hpc/software/Modules/3.2.9/modulefiles/FastTreeMP/2.1.10’, ‘MODULESHOME’: ‘/hpc/software/spack_v20d1/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lmod-8.7.24-ptfr7cudrme2v7y2nfktkkftnrgkezra/lmod/lmod’, ‘LMOD_SETTARG_FULL_SUPPORT’: ‘no’, ‘CONDA_DEFAULT_ENV’: ‘phylophlan’, ‘HISTSIZE’: ‘1000’, ‘LMOD_PKG’: ‘/hpc/software/spack_v20d1/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lmod-8.7.24-ptfr7cudrme2v7y2nfktkkftnrgkezra/lmod/lmod’, ‘LMOD_CMD’: ‘/hpc/software/spack_v20d1/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lmod-8.7.24-ptfr7cudrme2v7y2nfktkkftnrgkezra/lmod/lmod/libexec/lmod’, ‘SLURM_LOCALID’: ‘0’, ‘LESSOPEN’: ‘||/usr/bin/lesspipe.sh %s’, ‘LMOD_DIR’: ‘/hpc/software/spack_v20d1/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lmod-8.7.24-ptfr7cudrme2v7y2nfktkkftnrgkezra/lmod/lmod/libexec’, ‘BASH_FUNC_which%%’: ‘() { ( alias;\n eval ${which_declare} ) | /usr/bin/which --tty-only --read-alias --read-functions --show-tilde --show-dot $@\n}’, ‘BASH_FUNC_module%%’: '() { if [ -z “${LMOD_SH_DBG_ON+x}” ]; then\n case “$-” in \n vx)\n __lmod_sh_dbg=‘vx’\n ;;\n v)\n __lmod_sh_dbg=‘v’\n ;;\n x)\n __lmod_sh_dbg=‘x’\n ;;\n esac;\n fi;\n if [ -n “${__lmod_sh_dbg:-}” ]; then\n set +$__lmod_sh_dbg;\n echo “Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod’s output” 1>&2;\n fi;\n eval “$($LMOD_CMD shell “$@”)” && eval “$(${LMOD_SETTARG_CMD:-:} -s sh)”;\n __lmod_my_status=$?;\n if [ -n “${__lmod_sh_dbg:-}” ]; then\n echo “Shell debugging restarted” 1>&2;\n set -$__lmod_sh_dbg;\n fi;\n unset __lmod_sh_dbg;\n return $__lmod_my_status\n}’, ‘BASH_FUNC_ml%%’: ‘() { eval “$($LMOD_DIR/ml_cmd “$@”)”\n}’, ‘OMP_NUM_THREADS’: ‘3’}

I have tried to load FastTreeMP/2.1.10 as a separate module, but that hasn’t helped. Any ideas what I shoudl do?

Here is my script :

phylophlan \

-i ./Roseburia/\\

-o output_Roseburia \\

-d /projects/b1180/db/phylophlan/genera_db/s__Roseburia_hominis \\

-t a \\

-f references_config.cfg \\

--nproc 16 \\

--diversity low \\

--fast \\

--verbose