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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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[e] substitution matrix "pfasum60" not found in "phylophlan_substitution_matrices/" #76

Open linss123 opened 2 years ago

linss123 commented 2 years ago

Hi, I installed Phylophlan from conda in new enviroment and ran the following command: phylophlan -i metawrap_70_10_bins/ -d amphora2 --diversity medium -f ~/phylophlan/supertree_nt.cfg --output_folder tree_phylophlan/. But i got this:

[e] substitution matrix "pfasum60" not found in "phylophlan_substitution_matrices/"
Available substitution matrices in "phylophlan_substitution_matrices/":

and i checked in "miniconda3/env/phylophan/lib/python3.10/site-packages/phylophan/phylophan_subsitution_matrices", and the pfasum60 file and pfasum60.pkl file existed. What should i do to solve this error? Thanks a lot for your help.

fasnicar commented 2 years ago

Hi, do you also have a local phylophlan_substitution_matrices where you executed PhyloPhlAn? If so, that will override the package folder miniconda3/env/phylophan/lib/python3.10/site-packages/phylophan/phylophan_subsitution_matrices. Alternatively, you can use the --submat_folder param to specify the right path.

Many thanks, Francesco

linss123 commented 2 years ago

Thanks Fasnicar, this problems seemed to solve with your help. However, a new error appeared soon: i ran following command: phylophlan -i metawrap_70_10_bins/ -d amphora2 --diversity medium -f ~/phylophlan/supertree_nt.cfg --output_folder tree_phylophlan/ --submat_folder ~/phylophlan/phylophlan_substitution_matrices/ and got this :

[e] program not installed or not present in the system path
    command_line: java -jar astral-4.11.1/astral.4.11.1.jar -i astral-4.11.1/test_data/song_mammals.424.gene.tre
           stdin: None
          stdout: None
             env: {'LESSOPEN': '| /bin/lesspipe %s', 'CONDA_PROMPT_MODIFIER': '(phylophlan) ', 'USER': 'zms', 'LC_TIME': 'zh_CN.UTF-8', 'SSH_AGENT_PID': '7295', 'XDG_SESSION_TYPE': 'x11', 'SHLVL': '2', 'HOME': '/home/zms', 'CONDA_SHLVL': '2', 'GTK_MODULES': 'gail:atk-bridge', 'LC_MONETARY': 'zh_CN.UTF-8', 'DBUS_STARTER_BUS_TYPE': 'session', 'XRDP_PULSE_SOURCE_SOCKET': 'xrdp_chansrv_audio_in_socket_10', 'XRDP_PULSE_SINK_SOCKET': 'xrdp_chansrv_audio_out_socket_10', 'DBUS_SESSION_BUS_ADDRESS': 'unix:abstract=/tmp/dbus-y5qdFon4vW,guid=78b69b16548627c6ad27107d616eb2e1', 'COLORTERM': 'truecolor', '_CE_M': '', 'GNOME_KEYRING_CONTROL': '/home/zms/.cache/keyring-Y2XFB1', 'PULSE_SCRIPT': '/etc/xrdp/pulse/default.pa', 'IM_CONFIG_PHASE': '1', 'LOGNAME': 'zms', '_': '/home/zms/miniconda3/envs/phylophlan/bin/phylophlan', 'XDG_SESSION_CLASS': 'user', 'TERM': 'xterm-256color', 'XDG_SESSION_ID': 'c2', 'GNOME_DESKTOP_SESSION_ID': 'this-is-deprecated', '_CE_CONDA': '', 'PATH': '/home/zms/miniconda3/envs/phylophlan/bin:/home/zms/miniconda3/condabin:/sbin:/bin:/usr/bin:/usr/local/bin:/snap/bin:home/bowtie2-2.4.4-linux-x86_64', 'SESSION_MANAGER': 'local/zms-PowerEdge-T640:@/tmp/.ICE-unix/7304,unix/zms-PowerEdge-T640:/tmp/.ICE-unix/7304', 'XDG_MENU_PREFIX': 'gnome-', 'LC_ADDRESS': 'zh_CN.UTF-8', 'XRDP_SOCKET_PATH': '/run/xrdp/sockdir', 'GNOME_TERMINAL_SCREEN': '/org/gnome/Terminal/screen/5c7137ed_9d13_4cac_8e56_6cf2fc0295dd', 'DISPLAY': ':10.0', 'LANG': 'en_US.UTF-8', 'XDG_CURRENT_DESKTOP': 'GNOME', 'LC_TELEPHONE': 'zh_CN.UTF-8', 'CONDA_PREFIX_1': '/home/zms/miniconda3', 'XMODIFIERS': '@im=ibus', '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:*.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': ':1.180', 'SSH_AUTH_SOCK': '/home/zms/.cache/keyring-Y2XFB1/ssh', 'CONDA_PYTHON_EXE': '/home/zms/miniconda3/bin/python', 'UID': '1000', 'SHELL': '/bin/bash', 'LC_NAME': 'zh_CN.UTF-8', 'QT_ACCESSIBILITY': '1', 'LESSCLOSE': '/bin/lesspipe %s %s', 'XRDP_SESSION': '1', 'CONDA_DEFAULT_ENV': 'phylophlan', '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/zms/metaData/20210909_Data/merged/refine_mergedbins/ae', 'CONDA_EXE': '/home/zms/miniconda3/bin/conda', 'DBUS_STARTER_ADDRESS': 'unix:abstract=/tmp/dbus-y5qdFon4vW,guid=78b69b16548627c6ad27107d616eb2e1', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'LC_NUMERIC': 'zh_CN.UTF-8', 'CONDA_PREFIX': '/home/zms/miniconda3/envs/phylophlan', 'LC_PAPER': 'zh_CN.UTF-8', 'VTE_VERSION': '6003'}

i read some former issues pointing out this error can be fixed by editing config files. Would you mind telling me how to solve it? Thanks a lot.

fasnicar commented 2 years ago

Glad it worked!

The error with astral is known and not an error per see, actually. When you run a gene tree pipeline, ASTRAL cannot be automatically installed, so you need to manually install it and also manually configure the config file according to your specific installation, this is also reported in the wiki.

Thanks, Francesco

linss123 commented 2 years ago

Hi, a new issues occurred. I used configuration file generated from phylophlan_write_default_configs.sh, and ran with this command: phylophlan -i metawrap_70_10_bins/ -d amphora2 --diversity medium -f ~/phylophlan/supermatrix_nt.cfg --output_folder ae_tree/ --submat_folder ~/phylophlan/phylophlan_substitution_matrices/ but it pointed out this： [e] both db_dna and db_aa are None! I checked if [db_dna] existed in the supermatrix_nt.cfg and it did not miss [db_dna]. Here is:

[db_dna]
program_name = /home/zms/miniconda3/envs/phylophlan/bin/makeblastdb
params = -parse_seqids -dbtype nucl
input = -in
output = -out
version = -version
command_line = #program_name# #params# #input# #output#

I have no idea how to deal with this issues. What should i do to solve? Thanks a lot.

fasnicar commented 2 years ago

Hi, the problem is that you used the supermatrix_nt.cfg which contains standard settings for a nucleotide database (_nt, and also from the [dn_dna] section you posted you can see that the program called is makeblastdb), while the amphora2 database you specified in the PhyloPhlAn command is a set of proteins. So, you should use instead the supermatrix_aa.cfg config file which is suited for proteins database.

Thanks, Francesco