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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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[error] Command: raxmlHPC-PTHREADS-SSE3' returned non-zero exit status 255. #77

Closed Jimmyeric94 closed 2 years ago

Jimmyeric94 commented 2 years ago

when type following command:

''phylophlan -i 3 -d phylophlan --diversity low -f /home/jxm/miniconda3/envs/tree/lib/python3.9/site-packages/phylophlan/phylophlan_configs/supermatrix_aa.cfg -o 2 ''

But i got this: Inputs already checked Inputs already translated into markers Markers already aligned (key: "msa") Markers already trimmed Alignments already merged "2/3concatenated.aln" Phylogeny "/home/jxm/Desktop/1/2/3.tre" (or "RAxML*.3.tre") already built Polytomies already resolved Refining phylogeny "2/3_resolved.tre"

**[e] Command '['/home/jxm/miniconda3/envs/tree/bin/raxmlHPC-PTHREADS-SSE3', '-p', '1989', '-m', 'PROTCATLG', '-T', '2', '-t', '2/3_resolved.tre', '-w', '/home/jxm/Desktop/1/2', '-s', '2/3_concatenated.aln', '-n', '3_refined.tre']' returned non-zero exit status 255.

[e] error while executing command_line: /home/jxm/miniconda3/envs/tree/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m PROTCATLG -T 2 -t 2/3_resolved.tre -w /home/jxm/Desktop/1/2 -s 2/3_concatenated.aln -n 3_refined.tre stdin: None stdout: None* env: {'LESSOPEN': '| /usr/bin/lesspipe %s', 'CONDA_PROMPT_MODIFIER': '(tree) ', 'USER': 'jxm', 'LANGUAGE': 'en_US:en', 'LC_TIME': 'en_US.UTF-8', 'TEXTDOMAIN': 'im-config', 'XDG_SEAT': 'seat0', 'SSH_AGENT_PID': '2713', 'XDG_SESSION_TYPE': 'x11', 'SHLVL': '1', 'CONDA_SHLVL': '2', 'OLDPWD': '/home/jxm/Desktop/1/3', 'QT4_IM_MODULE': 'xim', 'HOME': '/home/jxm', 'DESKTOP_SESSION': 'ubuntu', 'GNOME_SHELL_SESSION_MODE': 'ubuntu', 'GTK_MODULES': 'gail:atk-bridge', 'LC_MONETARY': 'en_US.UTF-8', 'MANAGERPID': '2605', 'DBUS_STARTER_BUS_TYPE': 'session', 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1000/bus,guid=e5afa1a3fcf8f9f05f1557ac61b77468', 'COLORTERM': 'truecolor', '_CE_M': '', 'IM_CONFIG_PHASE': '2', 'LOGNAME': 'jxm', 'GTK_IM_MODULE': 'ibus', 'JOURNALSTREAM': '9:70754', '': '/home/jxm/miniconda3/envs/tree/bin/phylophlan', 'USERNAME': 'jxm', 'XDG_SESSION_ID': '3', 'TERM': 'xterm-256color', '_CE_CONDA': '', 'GNOME_DESKTOP_SESSION_ID': 'this-is-deprecated', 'WINDOWPATH': '2', 'PATH': '/home/jxm/miniconda3/envs/tree/bin:/home/jxm/miniconda3/condabin:/home/jxm/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'INVOCATION_ID': 'a14d30f01415462c8aebeafb056a29c6', 'PAPERSIZE': 'letter', 'SESSION_MANAGER': 'local/jimmy:@/tmp/.ICE-unix/2636,unix/jimmy:/tmp/.ICE-unix/2636', 'XDG_MENU_PREFIX': 'gnome-', 'GNOME_TERMINAL_SCREEN': '/org/gnome/Terminal/screen/7ce429c3_c281_4360_b1cc_2b70134b54bb', 'LC_ADDRESS': 'en_US.UTF-8', 'XDG_RUNTIME_DIR': '/run/user/1000', 'DISPLAY': ':1', 'ZEITGEIST_DATA_PATH': '/home/jxm/.local/share/zeitgeist', 'LANG': 'en_US.UTF-8', 'CONDA_PREFIX_1': '/home/jxm/miniconda3', 'XDG_CURRENT_DESKTOP': 'ubuntu:GNOME', 'LC_TELEPHONE': '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=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:.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:.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:', 'XDG_SESSION_DESKTOP': 'ubuntu', 'XMODIFIERS': '@im=ibus', 'GNOME_TERMINAL_SERVICE': ':1.389', 'XAUTHORITY': '/run/user/1000/gdm/Xauthority', 'SSH_AUTH_SOCK': '/run/user/1000/keyring/ssh', 'CONDA_PYTHON_EXE': '/home/jxm/miniconda3/bin/python', 'LC_NAME': 'en_US.UTF-8', 'SHELL': '/bin/bash', 'QT_ACCESSIBILITY': '1', 'GDMSESSION': 'ubuntu', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'CONDA_DEFAULT_ENV': 'tree', 'LC_MEASUREMENT': 'en_US.UTF-8', 'TEXTDOMAINDIR': '/usr/share/locale/', 'GPG_AGENT_INFO': '/run/user/1000/gnupg/S.gpg-agent:0:1', 'LC_IDENTIFICATION': 'en_US.UTF-8', 'XDG_VTNR': '2', 'QT_IM_MODULE': 'xim', 'PWD': '/home/jxm/Desktop/1', 'CLUTTER_IM_MODULE': 'xim', 'CONDA_EXE': '/home/jxm/miniconda3/bin/conda', 'XDG_DATA_DIRS': '/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop', 'DBUS_STARTER_ADDRESS': 'unix:path=/run/user/1000/bus,guid=e5afa1a3fcf8f9f05f1557ac61b77468', 'XDG_CONFIG_DIRS': '/etc/xdg/xdg-ubuntu:/etc/xdg', 'LC_NUMERIC': 'en_US.UTF-8', 'LC_PAPER': 'en_US.UTF-8', 'CONDA_PREFIX': '/home/jxm/miniconda3/envs/tree', 'VTE_VERSION': '5202'}

and i have checked the "raxmlHPC-PTHREADS-SSE3 -h

This is RAxML version 8.2.12 released by Alexandros Stamatakis on May 2018.

With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Sarah Lutteropp (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Charlie Taylor (UF) " What should i do to solve this error? Thanks a lot for your help.

fasnicar commented 2 years ago

Hi, it seems from the log that it is not the first time you ran that PhyloPhlAn command, correct? In which case I believe your RAxML error is due to the fact that RAxML finds already a RAxML output file (_info) and hence won't run. Two things, (1) have you tried running the command provided in the error message /home/jxm/miniconda3/envs/tree/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m PROTCATLG -T 2 -t 2/3_resolved.tre -w /home/jxm/Desktop/1/2 -s 2/3_concatenated.aln -n 3_refined.tre? and (2) have you check the output folder 2 to remove any RAxML related files?

Many thanks, Francesco

Jimmyeric94 commented 2 years ago

Dear Francesco: Thanks a lot. I have deleted all the running records and re-run the PhyloPhlAn command. It worked.

Yours Eric

从 Windows 版邮件https://go.microsoft.com/fwlink/?LinkId=550986发送

发件人: Francesco @.> 发送时间: 2021年12月27日 18:38 收件人: @.> 抄送: @.>; @.> 主题: Re: [biobakery/phylophlan] [error] Command: raxmlHPC-PTHREADS-SSE3' returned non-zero exit status 255. (Issue #77)

Hi, it seems from the log that it is not the first time you ran that PhyloPhlAn command, correct? In which case I believe your RAxML error is due to the fact that RAxML finds already a RAxML output file (_info) and hence won't run. Two things, (1) have you tried running the command provided in the error message /home/jxm/miniconda3/envs/tree/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m PROTCATLG -T 2 -t 2/3_resolved.tre -w /home/jxm/Desktop/1/2 -s 2/3_concatenated.aln -n 3_refined.tre? and (2) have you check the output folder 2 to remove any RAxML related files?

Many thanks, Francesco

― Reply to this email directly, view it on GitHubhttps://github.com/biobakery/phylophlan/issues/77#issuecomment-1001500204, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AXBHDF6KFK3ZPOMLD6RORCLUTA62FANCNFSM5KW25LCQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.Message ID: @.***>

TKsh6 commented 1 year ago

Hi, it seems from the log that it is not the first time you ran that PhyloPhlAn command, correct? In which case I believe your RAxML error is due to the fact that RAxML finds already a RAxML output file (_info) and hence won't run. Two things, (1) have you tried running the command provided in the error message /home/jxm/miniconda3/envs/tree/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m PROTCATLG -T 2 -t 2/3_resolved.tre -w /home/jxm/Desktop/1/2 -s 2/3_concatenated.aln -n 3_refined.tre? and (2) have you check the output folder 2 to remove any RAxML related files?

Many thanks, Francesco

Hi, I met the same problem and I ran the command 

phylophlan \
    -i mix_bins \
    -o mix_out \
    -d /beegfs/home/syl/database_db/PhyloPhlAn/phylophlan/phylophlan \
    --trim greedy \
    -t a \
    -f isolates_config.cfg \
    --diversity high \
    --nproc 4

with this error:


[e] Command '['/beegfs/home/syl/anaconda3/envs/phylophlan/bin/raxmlHPC-PTHREADS-SSE3', '-p', '1989', '-m', 'GTRCAT', '-T', '4', '-t', 'mix_out/mix_bins_resolved.tre', '-w', '/beegfs/home/syl/task_meta/mix_out', '-s', 'mix_out/mix_bins_concatenated.aln', '-n', 'mix_bins_refined.tre']' returned non-zero exit status 255.

[e] error while executing
    command_line: /beegfs/home/syl/anaconda3/envs/phylophlan/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m GTRCAT -T 4 -t mix_out/mix_bins_resolved.tre -w /beegfs/home/syl/task_meta/mix_out -s mix_out/mix_bins_concatenated.aln -n mix_bins_refined.tre
           stdin: None
          stdout: None
             env: {'SLURM_NODELIST': 'node15', 'MANPATH': '/beegfs/home/public/opt/lmod/lmod/share/man::/beegfs/root/openmpi-4.1.1/share/man', 'SLURM_JOB_NAME': 'phy', 'XDG_SESSION_ID': '11456', 'HOSTNAME': 'node15', 'SLURM_TOPOLOGY_ADDR': 'node15', 'SLURMD_NODENAME': 'node15', 'SLURM_PRIO_PROCESS': '0', 'SLURM_NODE_ALIASES': '(null)', 'TERM': 'xterm', 'SHELL': '/bin/bash', 'LMOD_ROOT': '/beegfs/home/public/opt/lmod', 'HISTSIZE': '1000', 'SLURM_JOB_QOS': 'normal', 'MODULEPATH_ROOT': '/beegfs/home/public/opt/modulefiles', 'SSH_CLIENT': '122.205.71.156 50537 26222', 'SLURM_TOPOLOGY_ADDR_PATTERN': 'node', 'TMPDIR': '/tmp', 'CONDA_SHLVL': '2', 'CONDA_PROMPT_MODIFIER': '(phylophlan) ', 'LMOD_PKG': '/beegfs/home/public/opt/lmod/lmod', 'EASYBUILD_PREFIX': '/beegfs/home/public/opt/easybuild', 'LMOD_VERSION': '8.7', 'SSH_TTY': '/dev/pts/16', 'SLURM_MEM_PER_CPU': '1783', 'USER': 'syl', 'SLURM_NNODES': '1', '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;05;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:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=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:*.jpg=01;35:*.jpeg=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:*.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:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=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:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:', 'LD_LIBRARY_PATH': ':/beegfs/root/openmpi-4.1.1/lib:/opt/MonitorSoftware/lib:/usr/sfw/lib:/usr/local/lib', 'LMOD_sys': 'Linux', 'CONDA_EXE': '/beegfs/home/syl/anaconda3/bin/conda', 'SLURM_JOBID': '343765', 'LIBPATH': ':/opt/MonitorSoftware/lib', '_CE_CONDA': '', 'CONDA_PREFIX_1': '/beegfs/home/syl/anaconda3', 'MAIL': '/var/spool/mail/syl', 'PATH': '/beegfs/home/syl/anaconda3/envs/phylophlan/bin:/beegfs/home/eggnog-mapper:/beegfs/home/syl/anaconda3/envs/eggnog-mapper/bin:/beegfs/home/syl/anaconda3/envs/eggnog-mapper/bin:/beegfs/home/syl/anaconda3/envs/eggnog-mapper/bin/emapper.py:/home/user/eggnog-mapper:/home/user/eggnog-mapper/eggnogmapper/bin:/beegfs/home/syl/software/FAPROTAX_1.2.6/collapse_table.py:/beegfs/home/syl/software/bamdst-master:/beegfs/home/syl/software/site-packages/lefse:/beegfs/home/syl/software/site-packages/lefse-1.1.2.dist-info:/beegfs/home/syl/software/site-packages/lefsebiom:/beegfs/home/syl/software/python-scripts:/beegfs/home/syl/software:/beegfs/home/syl/software/quast-5.2.0/bin:/beegfs/home/syl/software/soap/bin:/beegfs/home/syl/software/Trimmomatic-0.39:/beegfs/home/syl/software/metabat:/beegfs/home/syl/anaconda3/envs/kofamscan/bin:/beegfs/home/syl/software/metabat:/beegfs/home/syl/software:/beegfs/home/syl/software/ANIcalculator_v1:/beegfs/home/syl/software/mummer-4.0.0rc1:/beegfs/home/syl/software/mash-Linux64v2.3:/beegfs/home/syl/software/mash-Linux64v2.3:/beegfs/home/syl/software/RefineM-master/bin:/beegfs/home/syl/database_db/gtdb:/beegfs/home/syl/software/Checkm_data:/beegfs/home/syl/.aspera/connect/bin:/beegfs/home/syl/anaconda3/envs/eggnog-mapper/bin:/beegfs/home/syl/anaconda3/bin:/beegfs/home/syl/anaconda3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/beegfs/root/openmpi-4.1.1/bin:/beegfs/root/software/stubl-master/bin:/beegfs/root/software/pestat:/beegfs/root/software/GTX.Zip:/opt/ibutils/bin:/beegfs/home/syl/.local/bin:/beegfs/home/syl/bin', 'SLURM_TASKS_PER_NODE': '1', 'SLURM_CONF': '/var/spool/slurmd/conf-cache/slurm.conf', 'SLURM_WORKING_CLUSTER': 'bmb:admin:6817:9728:109', '_': '/beegfs/home/syl/anaconda3/envs/phylophlan/bin/phylophlan', 'SLURM_CPUS_PER_TASK': '4', 'SLURM_JOB_ID': '343765', 'CONDA_PREFIX': '/beegfs/home/syl/anaconda3/envs/phylophlan', 'PWD': '/beegfs/home/syl/task_meta', 'SLURM_JOB_USER': 'syl', 'LANG': 'en_US.UTF-8', 'MODULEPATH': '/beegfs/home/public/opt/easybuild/modules/bio:/beegfs/home/public/opt/PATH/bio/:/beegfs/home/public/opt/easybuild/modules/mpi:/beegfs/home/public/opt/easybuild/modules/all:/beegfs/home/public/opt/modulefiles/Linux:/beegfs/home/public/opt/modulefiles/Core:/beegfs/home/public/opt/lmod/lmod/modulefiles/Core', 'SLURM_JOB_UID': '1036', 'SLURM_NODEID': '0', 'SLURM_SUBMIT_DIR': '/beegfs/home/syl/task_meta', 'LMOD_CMD': '/beegfs/home/public/opt/lmod/lmod/libexec/lmod', 'SLURM_TASK_PID': '64798', 'SLURM_CPUS_ON_NODE': '4', '_CE_M': '', 'HISTCONTROL': 'ignoredups', 'ENVIRONMENT': 'BATCH', 'SLURM_PROCID': '0', 'SLURM_JOB_NODELIST': 'node15', 'SHLVL': '2', 'HOME': '/beegfs/home/syl', 'SLURM_LOCALID': '0', 'SLURM_CLUSTER_NAME': 'bmb', 'SLURM_JOB_CPUS_PER_NODE': '4', 'SLURM_JOB_GID': '1001', 'SLURM_SUBMIT_HOST': 'login', 'SLURM_GTIDS': '0', 'STUBL_HOME': '/beegfs/root/software/stubl-master', 'BASH_ENV': '/beegfs/home/public/opt/lmod/lmod/init/bash', 'SLURM_JOB_PARTITION': 'normal', 'CONDA_PYTHON_EXE': '/beegfs/home/syl/anaconda3/bin/python', 'LOGNAME': 'syl', 'XDG_DATA_DIRS': '/beegfs/home/syl/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share', 'SSH_CONNECTION': '122.205.71.156 50537 122.205.95.197 26222', 'MODULESHOME': '/beegfs/home/public/opt/lmod/lmod', 'SLURM_JOB_NUM_NODES': '1', 'CONDA_DEFAULT_ENV': 'phylophlan', 'LESSOPEN': '||/usr/bin/lesspipe.sh %s', 'LMOD_SETTARG_FULL_SUPPORT': 'no', 'SHLIB_PATH': ':/opt/MonitorSoftware/lib', 'XDG_RUNTIME_DIR': '/run/user/1036', 'DISPLAY': 'localhost:24.0', 'LMOD_DIR': '/beegfs/home/public/opt/lmod/lmod/libexec', 'BASH_FUNC_module()': '() {  local __lmod_my_status;\n local __lmod_sh_dbg;\n if [ -z "${LMOD_SH_DBG_ON+x}" ]; then\n case "$-" in \n *v*x*)\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 bash "$@")" && 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 return $__lmod_my_status\n}', 'BASH_FUNC_ml()': '() {  eval "$($LMOD_DIR/ml_cmd "$@")"\n}'}

so I ran this command: raxmlHPC-PTHREADS-SSE3 -p 1989 -m GTRCAT -T 4 -t mix_out/mix_bins_resolved.tre -w /beegfs/home/syl/task_meta/mix_out -s mix_out/mix_bins_concatenated.aln -n mix_bins_refined.tre but I got this:

Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!

RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file

ERROR: Bad base (L) at site 27 of sequence 1

How can I do to solve this ?

sentausa commented 1 year ago

@TKsh6 I believe you can try the solution proposed in https://github.com/biobakery/phylophlan/issues/91

TKsh6 commented 1 year ago

@sentausa Thank you ! I have made it.