Refine_gene_tree crashed

[Valentin-Bio]

Hello Developer, I ran Phylophlan over a set of 1100 metagenome assembled genomes under the following configuration:

phylophlan -i derep_genomes -o phylophlan_output -t a --nproc 30 --accurate --genome_extension .fa --diversity high -d phylophlan \
        -f /home/vberrios/phylophlan_config_files/supertree_aa.cfg --maas /home/vberrios/mis_cosas/antartica/MAGs/arranged/sub_models.tsv

I have used one of the standard configuration files (.cfg) that were available and the subtitution model tsv file that you provide.

And got the following error message:

[e] error while refining gene tree
{'program_name': '/opt/miniconda/miniconda-py312_24.3.0-0/envs/phylophlan/bin/raxmlHPC', 'params': '-p 1989', 'database': '-t', 'input': '-s', 'output_path': '-w', 'output': '-n', 'version': '-v', 'model': '-m', 'command_line': '#program_name# #model# #params# #database# #output_path# #input# #output#'}
PROTCATRTREV
phylophlan_output/tmp/sub/p0194.aln
phylophlan_output/tmp/gene_tree1_polytomies/p0194.tre
/home/vberrios/mis_cosas/antartica/MAGs/arranged/phylophlan_output/tmp/gene_tree2
p0194.tre

[e] Command '['/opt/miniconda/miniconda-py312_24.3.0-0/envs/phylophlan/bin/raxmlHPC', '-m', 'PROTCATRTREV', '-p', '1989', '-t', 'phylophlan_output/tmp/gene_tree1_polytomies/p0230.tre', '-w', '/home/vberrios/mis_cosas/antartica/MAGs/arranged/phylophlan_output/tmp/gene_tree2', '-s', 'phylophlan_output/tmp/sub/p0230.aln', '-n', 'p0230.tre']' returned non-zero exit status 255.

[e] error while executing
command_line: /opt/miniconda/miniconda-py312_24.3.0-0/envs/phylophlan/bin/raxmlHPC -m PROTCATRTREV -p 1989 -t phylophlan_output/tmp/gene_tree1_polytomies/p0230.tre -w /home/vberrios/mis_cosas/antartica/MAGs/arranged/phylophlan_output/tmp/gene_tree2 -s phylophlan_output/tmp/sub/p0230.aln -n p0230.tre
stdin: None
stdout: None
env: {'SHELL': '/bin/bash', 'SLURM_JOB_USER': 'vberrios', 'SLURM_TASKS_PER_NODE': '1', 'SLURM_JOB_UID': '1002', 'HISTCONTROL': 'ignoredups', 'SLURM_TASK_PID': '252708', 'CONDA_EXE': '/opt/miniconda/miniconda-py312_24.3.0-0/bin/conda', 'SLURM_LOCALID': '0', 'SLURM_SUBMIT_DIR': '/home/vberrios/mis_cosas/antartica/MAGs/arranged', 'HISTSIZE': '1000', 'HOSTNAME': 'n001', 'SLURMD_NODENAME': 'n001', 'FPATH': '/usr/share/lmod/lmod/init/ksh_funcs', 'SLURM_JOB_START_TIME': '1740763666', 'HYDRA_LAUNCHER_EXTRA_ARGS': '--external-launcher', 'JAVA_HOME': ':-', 'ModuleTable002': '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', '__LMOD_REF_COUNT_MODULEPATH': '/etc/modulefiles:1;/usr/share/modulefiles:1;/opt/modulefiles:1;/opt/intel/oneapi/modulefiles:1;/usr/share/modulefiles/Linux:1;/usr/share/modulefiles/Core:1;/usr/share/lmod/lmod/modulefiles/Core:1', 'JAVA_LD_LIBRARY_PATH': ':-', 'SLURM_CLUSTER_NAME': '(null)', 'SLURM_JOB_END_TIME': '1741404466', 'SLURM_CPUS_ON_NODE': '30', 'SLURM_JOB_CPUS_PER_NODE': '30', 'LMOD_DIR': '/usr/share/lmod/lmod/libexec', 'PWD': '/home/vberrios/mis_cosas/antartica/MAGs/arranged', 'PRTE_MCA_plm_slurm_args': '--external-launcher', 'SLURM_GTIDS': '0', 'LOGNAME': 'vberrios', 'XDG_SESSION_TYPE': 'tty', 'CONDA_PREFIX': '/home/vberrios/.conda/envs/phylophlan', 'SLURM_JOB_PARTITION': 'basic', 'MODULESHOME': '/usr/share/lmod/lmod', 'MAMBA_ROOT_PREFIX': '/home/vberrios/.local/share/mamba', 'MANPATH': '/usr/share/lmod/lmod/share/man:', 'SLURM_TRES_PER_TASK': 'cpu:30', 'SLURM_JOB_NUM_NODES': '1', '_': '/home/vberrios/.conda/envs/phylophlan/bin/phylophlan', 'SLURM_JOBID': '16842', 'I_MPI_HYDRA_BOOTSTRAP_EXEC_EXTRA_ARGS': '--external-launcher', 'SLURM_JOB_QOS': 'normal', 'MOTD_SHOWN': 'pam', '__LMOD_REF_COUNT_PATH': '/opt/miniconda/miniconda-py312_24.3.0-0/bin:1;/home/vberrios/.local/share/mamba/condabin:1;/home/vberrios/.local/bin:1;/home/vberrios/bin:1;/usr/local/bin:1;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;/usr/lib64/mpich/lib:1', 'HOME': '/home/vberrios', 'ModuleTable_Sz': '3', 'LANG': 'en_US.UTF-8', '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;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:.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=01;36:.au=01;36:.flac=01;36:.m4a=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:.oga=01;36:.opus=01;36:.spx=01;36:.xspf=01;36:', 'SLURM_PROCID': '0', 'LMOD_SETTARG_FULL_SUPPORT': 'no', 'CONDA_PROMPT_MODIFIER': '(phylophlan) ', 'TMPDIR': '/tmp', 'SLURM_CPUS_PER_TASK': '30', 'SLURM_TOPOLOGY_ADDR': 'n001', 'LMOD_VERSION': '8.7.32', 'SSH_CONNECTION': '190.114.34.114 28170 10.0.0.2 22', 'ModuleTable003': 'dWxlZmlsZXMvQ29yZSIsCn0K', 'HYDRA_BOOTSTRAP': 'slurm', 'MODULEPATH_ROOT': '/usr/share/modulefiles', 'SLURM_TOPOLOGY_ADDR_PATTERN': 'node', 'XDG_SESSION_CLASS': 'user', 'LMOD_PKG': '/usr/share/lmod/lmod', 'SLURM_MEM_PER_NODE': '10240', 'MAMBA_EXE': '/opt/miniconda/miniconda-py312_24.3.0-0/bin/mamba', 'TERM': 'xterm-256color', 'LESSOPEN': '||/usr/bin/lesspipe.sh %s', 'USER': 'vberrios', 'SLURM_NODELIST': 'n001', 'ENVIRONMENT': 'BATCH', 'CONDA_SHLVL': '2', 'LOADEDMODULES': 'Miniconda/py312_24.3.0-0', 'SLURM_JOB_ACCOUNT': 'root', 'SLURM_PRIO_PROCESS': '0', 'LMOD_ROOT': '/usr/share/lmod', 'SHLVL': '2', 'SLURM_NNODES': '1', 'BASH_ENV': '/usr/share/lmod/lmod/init/bash', 'LMOD_sys': 'Linux', 'XDG_SESSION_ID': '33', 'SLURM_SUBMIT_HOST': 'maccartney-front', 'ModuleTable001': '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', 'CONDA_PYTHON_EXE': '/opt/miniconda/miniconda-py312_24.3.0-0/bin/python', 'LD_LIBRARY_PATH': ':/usr/lib64/mpich/lib', 'XDG_RUNTIME_DIR': '/run/user/1002', 'SLURM_JOB_ID': '16842', 'SLURM_NODEID': '0', 'SSH_CLIENT': '190.114.34.114 28170 22', 'CONDA_DEFAULT_ENV': 'phylophlan', 'DEBUGINFOD_URLS': 'https://debuginfod.centos.org/ ', 'which_declare': 'declare -f', 'SLURM_CONF': '/etc/slurm/slurm.conf', 'PATH': '/home/vberrios/.conda/envs/phylophlan/bin:/opt/miniconda/miniconda-py312_24.3.0-0/bin:/home/vberrios/.local/share/mamba/condabin:/home/vberrios/.local/bin:/home/vberrios/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/mpich/lib', 'SLURM_JOB_NAME': 'phylophlan', 'MODULEPATH': '/etc/modulefiles:/usr/share/modulefiles:/opt/modulefiles:/opt/intel/oneapi/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core', 'LMFILES': '/opt/modulefiles/Miniconda/py312_24.3.0-0.lua', 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1002/bus', 'LMOD_CMD': '/usr/share/lmod/lmod/libexec/lmod', 'MAIL': '/var/spool/mail/vberrios', 'SSH_TTY': '/dev/pts/3', 'CONDA_PREFIX_1': '/opt/miniconda/miniconda-py312_24.3.0-0', 'OMPI_MCA_plm_slurm_args': '--external-launcher', 'SLURM_JOB_GID': '100', 'OLDPWD': '/home/vberrios/mis_cosas/antartica/MAGs', 'SLURM_JOB_NODELIST': 'n001', 'I_MPI_HYDRA_BOOTSTRAP': 'slurm', 'BASH_FUNC_ml%%': '() { eval "$($LMOD_DIR/ml_cmd "$@")"\n}', '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}'}

[e] Command '['/opt/miniconda/miniconda-py312_24.3.0-0/envs/phylophlan/bin/raxmlHPC', '-m', 'PROTCATRTREV', '-p', '1989', '-t', 'phylophlan_output/tmp/gene_tree1_polytomies/p0230.tre', '-w', '/home/vberrios/mis_cosas/antartica/MAGs/arranged/phylophlan_output/tmp/gene_tree2', '-s', 'phylophlan_output/tmp/sub/p0230.aln', '-n', 'p0230.tre']' returned non-zero exit status 255.

[e] error while refining gene tree
{'program_name': '/opt/miniconda/miniconda-py312_24.3.0-0/envs/phylophlan/bin/raxmlHPC', 'params': '-p 1989', 'database': '-t', 'input': '-s', 'output_path': '-w', 'output': '-n', 'version': '-v', 'model': '-m', 'command_line': '#program_name# #model# #params# #database# #output_path# #input# #output#'}
PROTCATRTREV
phylophlan_output/tmp/sub/p0230.aln
phylophlan_output/tmp/gene_tree1_polytomies/p0230.tre
/home/vberrios/mis_cosas/antartica/MAGs/arranged/phylophlan_output/tmp/gene_tree2
p0230.tre

[e] Command '['/opt/miniconda/miniconda-py312_24.3.0-0/envs/phylophlan/bin/raxmlHPC', '-m', 'PROTCATLG', '-p', '1989', '-t', 'phylophlan_output/tmp/gene_tree1_polytomies/p0170.tre', '-w', '/home/vberrios/mis_cosas/antartica/MAGs/arranged/phylophlan_output/tmp/gene_tree2', '-s', 'phylophlan_output/tmp/sub/p0170.aln', '-n', 'p0170.tre']' returned non-zero exit status 255.

[e] refine_gene_tree crashed