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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] resolve_polytomies crashed #54

Open myoreo777 opened 3 years ago

myoreo777 commented 3 years ago

Dear phylophlan team,

I've installed PhyloPhlAn 3 from conda, and run the following command:

phylophlan -i /home/mwa/input_phylophlan -t a -d phylophlan -f supermatrix_aa.cfg --diversity medium --nproc 4 --min_num_proteins 1 --min_len_protein 10 --min_num_entries 1 --verbose

and the output is:

PhyloPhlAn version 3.0.58 (8 September 2020)

Command line: /home/mwa/miniconda3/envs/phylophlan/bin/phylophlan -i /home/mwa/input_phylophlan -t a -d phylophlan -f supermatrix_aa.cfg --diversity medium --nproc 4 --min_num_proteins 1 --min_len_protein 10 --min_num_entries 1 --verbose

Automatically setting "input=input_phylophlan" and "input_folder=/home/mwa" "medium-accurate" preset Setting "sort=True" because "database=phylophlan" Setting "min_num_markers=100" since no value has been specified and the "database=phylophlan" Arguments: {'input': 'input_phylophlan', 'clean': None, 'output': 'input_phylophlan_phylophlan', 'database': 'phylophlan', 'db_type': 'a', 'config_file': 'supermatrix_aa.cfg', 'diversity': 'medium', 'accurate': True, 'fast': False, 'clean_all': False, 'database_list': False, 'submat': 'pfasum60', 'submat_list': False, 'submod_list': False, 'nproc': 4, 'min_num_proteins': 1, 'min_len_protein': 10, 'min_num_markers': 100, 'trim': 'gap_trim', 'gap_perc_threshold': 0.67, 'not_variant_threshold': 0.99, 'subsample': <function onehundred at 0x7f03546ea820>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x7f03546eab80>, 'sort': True, 'remove_fragmentary_entries': False, 'fragmentary_threshold': 0.85, 'min_num_entries': 1, 'maas': None, 'remove_only_gaps_entries': False, 'mutation_rates': False, 'force_nucleotides': False, 'input_folder': '/home/mwa/input_phylophlan', 'data_folder': 'input_phylophlan_phylophlan/tmp', 'databases_folder': 'phylophlan_databases/', 'submat_folder': '/home/mwa/miniconda3/envs/phylophlan/lib/python3.9/site-packages/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': '/home/mwa/miniconda3/envs/phylophlan/lib/python3.9/site-packages/phylophlan/phylophlan_substitution_models/', 'configs_folder': 'phylophlan_configs/', 'output_folder': '', 'genome_extension': '.fna', 'proteome_extension': '.faa', 'update': False, 'verbose': True} Loading configuration file "supermatrix_aa.cfg" Checking configuration file Checking "/home/mwa/miniconda3/bin/diamond" Checking "/home/mwa/miniconda3/bin/mafft" Checking "/home/mwa/miniconda3/bin/trimal" Checking "/home/mwa/miniconda3/bin/FastTreeMP" Checking "/home/mwa/miniconda3/bin/raxmlHPC-PTHREADS-SSE3" "db_aa" database "phylophlan_databases/phylophlan/phylophlan.dmnd" present Loading files from "/home/mwa/input_phylophlan" Loading files from "/home/mwa/input_phylophlan" Inputs already checked Loading checked inputs from "input_phylophlan_phylophlan/tmp/checked_inputs.pkl" Inputs already cleaned Loading files from "input_phylophlan_phylophlan/tmp/clean_aa" "phylophlan" markers already mapped (key: "map_aa") Markers already selected Markers already extracted Inputs already translated into markers Markers already aligned (key: "msa") Markers already trimmed (key: "trim") Substitution matrix "/home/mwa/miniconda3/envs/phylophlan/lib/python3.9/site-packages/phylophlan/phylophlan_substitution_matrices/pfasum60.pkl" loaded Markers already subsampled Alignments already merged "input_phylophlan_phylophlan/input_phylophlan_concatenated.aln" Phylogeny "/home/mwa/input_phylophlan_phylophlan/inputphylophlan.tre" (or "RAxML*.input_phylophlan.tre") already built Resolving 1 polytomies Resolving polytomies for "input_phylophlan_phylophlan/input_phylophlan.tre"

[e] Error parsing data source 'input_phylophlan_phylophlan/input_phylophlan.tre' on line 1 at column 0: Unexpected end of stream

[e] error while resolving polytomies input_phylophlan_phylophlan/input_phylophlan.tre input_phylophlan_phylophlan/input_phylophlan_resolved.tre

[e] Error sending result: '<multiprocessing.pool.ExceptionWithTraceback object at 0x7f03546499d0>'. Reason: 'TypeError("cannot pickle '_io.TextIOWrapper' object")'

[e] resolve_polytomies crashed

What should I do next? Thanks a lot for your help.

fasnicar commented 3 years ago

Hi, thanks for reporting this and for using PhyloPhlAn.

From the log you posted, it is clear that this is not the first time you run PhyloPhlAn on these inputs. So one thing I would check first is if the input_phylophlan_phylophlan/input_phylophlan.tre phylogeny built in a previous run is a valid phylogeny. If not you can remove it and PhyloPhlAn will re-build it starting from the MSA already computed.

myoreo777 commented 3 years ago

Hi Francesco, I removed the file 'input_phylophlan_phylophlan' and ran the same command again. The first few steps all worked fine, but in the end several errors appeared

[e] Command '['/home/mwa/miniconda3/bin/FastTreeMP', '-quiet', '-pseudo', '-spr', '4', '-mlacc', '2', '-slownni', '-fastest', '-no2nd', '-mlnni', '4', '-lg', '-out', '/home/mwa/input_phylophlan_phylophlan/input_phylophlan.tre', 'input_phylophlan_phylophlan/input_phylophlan_concatenated.aln']' returned non-zero exit status 1.

[e] error while executing command_line: /home/mwa/miniconda3/bin/FastTreeMP -quiet -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /home/mwa/input_phylophlan_phylophlan/input_phylophlan.tre input_phylophlan_phylophlan/input_phylophlan_concatenated.aln stdin: None stdout: None env: {'LESSOPEN': '| /usr/bin/lesspipe %s', 'CONDA_PROMPT_MODIFIER': '(phylophlan) ', 'USER': 'mwa', 'GIT_ASKPASS': '/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/extensions/git/dist/askpass.sh', 'USES_VSCODE_SERVER_SPAWN': 'true', 'SHLVL': '1', 'BROWSER': '/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/bin/helpers/browser.sh', 'MOTD_SHOWN': 'update-motd', 'HOME': '/home/mwa', 'CONDA_SHLVL': '2', 'TERM_PROGRAM_VERSION': '1.52.1', 'VSCODE_IPC_HOOK_CLI': '/tmp/vscode-ipc-fecd5993-e2a9-48e5-b94e-77eab76646c9.sock', 'VSCODE_GIT_ASKPASS_MAIN': '/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/extensions/git/dist/askpass-main.js', 'VSCODE_GIT_ASKPASS_NODE': '/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/node', 'COLORTERM': 'truecolor', '_CE_M': '', 'WSL_DISTRO_NAME': 'Ubuntu', 'PIPELOGGING': 'true', 'LOGNAME': 'mwa', 'NAME': 'LAPTOP-R23JDN0Q', '': '/home/mwa/miniconda3/envs/phylophlan/bin/phylophlan', 'TERM': 'xterm-256color', '_CE_CONDA': '', 'PATH': '/home/mwa/miniconda3/envs/phylophlan/bin:/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/bin:/home/mwa/miniconda3/bin:/home/mwa/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files (x86)/Common Files/Oracle/Java/javapath:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program Files/Intel/WiFi/bin:/mnt/c/Program Files/Common Files/Intel/WirelessCommon:/mnt/c/Program Files (x86)/Common Files/Autodesk Shared:/mnt/c/Program Files (x86)/backburner 2:/mnt/c/Program Files/NCBI/blast-2.10.1+/bin:/mnt/c/Users/Maothilda/AppData/Local/Microsoft/WindowsApps:/mnt/c/Program Files/Bandizip:/mnt/c/Users/Maothilda/AppData/Local/Programs/Microsoft VS Code/bin:/snap/bin', 'LANG': 'C.UTF-8', 'CONDA_PREFIX_1': '/home/mwa/miniconda3', '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:', 'VSCODE_GIT_IPC_HANDLE': '/tmp/vscode-git-1fcf238dea.sock', 'TERM_PROGRAM': 'vscode', 'CONDA_PYTHON_EXE': '/home/mwa/miniconda3/bin/python', 'SHELL': '/bin/bash', 'VERBOSE_LOGGING': 'true', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'CONDA_DEFAULT_ENV': 'phylophlan', 'PWD': '/home/mwa', 'CONDA_EXE': '/home/mwa/miniconda3/bin/conda', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'AMD_ENTRYPOINT': 'vs/server/remoteExtensionHostProcess', 'CONDA_PREFIX': '/home/mwa/miniconda3/envs/phylophlan', 'HOSTTYPE': 'x86_64', 'WSLENV': 'VSCODE_WSL_EXT_LOCATION/up', 'OMP_NUM_THREADS': '3'}

In fact, this happened before I encountered the last error

fasnicar commented 3 years ago

Ok, thanks, then something is not right with the MSA probably. Have you tried run the FastTree command in the error:

/home/mwa/miniconda3/bin/FastTreeMP -pseudo -spr 4 -mlacc 2 -slownni -fastest -no2nd -mlnni 4 -lg -out /home/mwa/input_phylophlan_phylophlan/input_phylophlan.tre input_phylophlan_phylophlan/input_phylophlan_concatenated.aln

(I just removed the -quiet parameter)

myoreo777 commented 3 years ago

I ran as you suggested and here's the output：

FastTree Version 2.1.10 Double precision (No SSE3), OpenMP (8 threads) Alignment: input_phylophlan_phylophlan/input_phylophlan_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 Error reading header line

fasnicar commented 3 years ago

Ok, can you check then that the MSA is a valid one? If not, probably something went wrong the first time you ran PhyloPhlAn and then I would suggest you remove the output folder and re-run the analysis from scratch. Before doing this, please check that the PhyloPhlAn version you're running is the latest one (3.0.60), if not, please update it to the latest. Thank you

myoreo777 commented 3 years ago

Hi Francesco, I updated the version of the software and tried to run the previous command. At first everything was fine,

`PhyloPhlAn version 3.0.60 (27 November 2020)

Command line: /home/mwa/miniconda3/bin/phylophlan -i /home/mwa/input_phylophlan -t a -d phylophlan -f supermatrix_aa.cfg --diversity medium --nproc 4 --min_num_entries 1 --verbose

Automatically setting "input=input_phylophlan" and "input_folder=/home/mwa" "medium-accurate" preset Setting "sort=True" because "database=phylophlan" Setting "min_num_markers=100" since no value has been specified and the "database=phylophlan" Arguments: {'input': 'input_phylophlan', 'clean': None, 'output': 'input_phylophlan_phylophlan', 'database': 'phylophlan', 'db_type': 'a', 'config_file': 'supermatrix_aa.cfg', 'diversity': 'medium', 'accurate': True, 'fast': False, 'clean_all': False, 'database_list': False, 'submat': 'pfasum60', 'submat_list': False, 'submod_list': False, 'nproc': 4, 'min_num_proteins': 1, 'min_len_protein': 50, 'min_num_markers': 100, 'trim': 'gap_trim', 'gap_perc_threshold': 0.67, 'not_variant_threshold': 0.99, 'subsample': <function onehundred at 0x7f5cbb057ef0>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x7f5cbb060290>, 'sort': True, 'remove_fragmentary_entries': False, 'fragmentary_threshold': 0.85, 'min_num_entries': 1, 'maas': None, 'remove_only_gaps_entries': False, 'mutation_rates': False, 'force_nucleotides': False, 'input_folder': '/home/mwa/input_phylophlan', 'data_folder': 'input_phylophlan_phylophlan/tmp', 'databases_folder': 'phylophlan_databases/', 'submat_folder': '/home/mwa/miniconda3/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': '/home/mwa/miniconda3/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_models/', 'configs_folder': 'phylophlan_configs/', 'output_folder': '', 'genome_extension': '.fna', 'proteome_extension': '.faa', 'update': False, 'verbose': True} Loading configuration file "supermatrix_aa.cfg" Checking configuration file Checking "/home/mwa/miniconda3/bin/diamond" Checking "/home/mwa/miniconda3/bin/mafft" Checking "/home/mwa/miniconda3/bin/trimal" Checking "/home/mwa/miniconda3/bin/FastTreeMP" Checking "/home/mwa/miniconda3/bin/raxmlHPC-PTHREADS-SSE3" "db_aa" database "phylophlan_databases/phylophlan/phylophlan.dmnd" present Loading files from "/home/mwa/input_phylophlan" Loading files from "/home/mwa/input_phylophlan" Inputs already checked Loading checked inputs from "input_phylophlan_phylophlan/tmp/checked_inputs.pkl" Inputs already cleaned Loading files from "input_phylophlan_phylophlan/tmp/clean_aa" "phylophlan" markers already mapped (key: "map_aa") Markers already selected Markers already extracted Inputs already translated into markers Markers already aligned (key: "msa") Markers already trimmed (key: "trim") Substitution matrix "/home/mwa/miniconda3/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_matrices/pfasum60.pkl" loaded Subsampling 332 markers Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0000.aln" Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0001.aln" Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0002.aln" Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0003.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0002.aln" Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0004.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0000.aln" Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0005.aln"`

but in the end there was an error like this `Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0393.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0386.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0392.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0390.aln" Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0394.aln" Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0395.aln" Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0397.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0393.aln" Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0399.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0397.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0399.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0395.aln" Removing generated empty MSAs "input_phylophlan_phylophlan/tmp/sub/p0394.aln" Concatenating alignments

[e] No alignments found to concatenate`

Thank you very much for your answer

fasnicar commented 3 years ago

Hi, how many inputs do you have in your input folders /home/mwa/input_phylophlan?

myoreo777 commented 3 years ago

There is only one amino acid sequence file in faa format in the input folder

fasnicar commented 3 years ago

Ok, so that's the problem. You can't build a phylogeny with only one single genome/proteome.

myoreo777 commented 3 years ago

This time I put three faa format amino acid sequence files in the input folder, but in the end an error occurred

Subsampling "input_phylophlan_phylophlan/tmp/trim_gap_trim/p0399.aln" "input_phylophlan_phylophlan/tmp/sub/p0390.aln" generated in 0s "input_phylophlan_phylophlan/tmp/sub/p0397.aln" generated in 0s "input_phylophlan_phylophlan/tmp/sub/p0399.aln" generated in 0s "input_phylophlan_phylophlan/tmp/sub/p0395.aln" generated in 0s Concatenating alignments Alignments concatenated "input_phylophlan_phylophlan/input_phylophlan_concatenated.aln" in 0s Building phylogeny "input_phylophlan_phylophlan/input_phylophlan_concatenated.aln" Phylogeny "input_phylophlan.tre" built in 1s Resolving 1 polytomies Resolving polytomies for "input_phylophlan_phylophlan/input_phylophlan.tre" "input_phylophlan_phylophlan/input_phylophlan_resolved.tre" generated in 0s Refining phylogeny "input_phylophlan_phylophlan/input_phylophlan_resolved.tre" [e] Command '['/home/mwa/miniconda3/bin/raxmlHPC-PTHREADS-SSE3', '-p', '1989', '-m', 'PROTCATLG', '-T', '4', '-t', 'input_phylophlan_phylophlan/input_phylophlan_resolved.tre', '-w', '/home/mwa/input_phylophlan_phylophlan', '-s', 'input_phylophlan_phylophlan/input_phylophlan_concatenated.aln', '-n', 'input_phylophlan_refined.tre']' returned non-zero exit 255. [e] error while executing command_line: /home/mwa/miniconda3/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m PROTCATLG -T 4 -t input_phylophlan_phylophlan/input_phylophlan_resolved.tre -w /home/mwa/input_phylophlan_phylophlan -s input_phylophlan_phylophlan/input_phylophlan_concatenated.aln -n input_phylophlan_refined.tre stdin: None
stdout: None env: {'LESSOPEN': '| /usr/bin/lesspipe %s', 'CONDA_PROMPT_MODIFIER': '(base) ', 'USER': 'mwa', 'GIT_ASKPASS': '/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/extensions/git/dist/askpass.sh', 'USES_VSCODE_SERVER_SPAWN': 'true', 'SHLVL': '1', 'BROWSER': '/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/bin/helpers/browser.sh', 'MOTD_SHOWN': 'update-motd', 'HOME': '/home/mwa', 'CONDA_SHLVL': '1', 'TERM_PROGRAM_VERSION': '1.52.1', 'VSCODE_IPC_HOOK_CLI': '/tmp/vscode-ipc-fecd5993-e2a9-48e5-b94e-77eab76646c9.sock', 'VSCODE_GIT_ASKPASS_MAIN': '/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/extensions/git/dist/askpass-main.js', 'VSCODE_GIT_ASKPASS_NODE': '/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/node', 'COLORTERM': 'truecolor', '_CE_M': '', 'WSL_DISTRO_NAME': 'Ubuntu', 'PIPELOGGING': 'true', 'LOGNAME': 'mwa', 'NAME': 'LAPTOP-R23JDN0Q', '': '/home/mwa/miniconda3/bin/phylophlan', 'TERM': 'xterm-256color', '_CE_CONDA': '', 'PATH': '/home/mwa/miniconda3/bin:/home/mwa/miniconda3/bin:/home/mwa/.vscode-server/bin/ea3859d4ba2f3e577a159bc91e3074c5d85c0523/bin:/home/mwa/miniconda3/bin:/home/mwa/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files (x86)/Common Files/Oracle/Java/javapath:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program Files/Intel/WiFi/bin:/mnt/c/Program Files/Common Files/Intel/WirelessCommon:/mnt/c/Program Files (x86)/Common Files/Autodesk Shared:/mnt/c/Program Files (x86)/backburner 2:/mnt/c/Program Files/NCBI/blast-2.10.1+/bin:/mnt/c/Users/Maothilda/AppData/Local/Microsoft/WindowsApps:/mnt/c/Program Files/Bandizip:/mnt/c/Users/Maothilda/AppData/Local/Programs/Microsoft VS Code/bin:/snap/bin', 'LANG': 'C.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:.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:', 'VSCODE_GIT_IPC_HANDLE': '/tmp/vscode-git-1fcf238dea.sock', 'TERM_PROGRAM': 'vscode', 'CONDA_PYTHON_EXE': '/home/mwa/miniconda3/bin/python', 'SHELL': '/bin/bash', 'VERBOSE_LOGGING': 'true', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'CONDA_DEFAULT_ENV': 'base', 'PWD': '/home/mwa', 'CONDA_EXE': '/home/mwa/miniconda3/bin/conda', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'AMD_ENTRYPOINT': 'vs/server/remoteExtensionHostProcess', 'CONDA_PREFIX': '/home/mwa/miniconda3', 'HOSTTYPE': 'x86_64', 'WSLENV': 'VSCODE_WSL_EXT_LOCATION/up'}

After that I entered：

/home/mwa/miniconda3/bin/raxmlHPC-PTHREADS-SSE3 -p 1989 -m PROTCATLG -T 4 -t input_phylophlan_phylophlan/input_phylophlan_resolved.tre -w /home/mwa/input_phylophlan_phylophlan -s input_phylophlan_phylophlan/input_phylophlan_concatenated.aln -n input_phylophlan_refined.tre

the output is:

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 TOO FEW SPECIES

I'd like to know at least how many input files are needed to meet the requirements. Thanks a lot.

fasnicar commented 3 years ago

Hi, the minimum number of genomes to build a phylogeny is 4. There should be a check, but to control this, but I'll have a look why it not providing the proper error message. Thanks